CEO Jed York took to the 49ers’ flagship radio station Tuesday morning and fielded an onslaught of aggressive questions from KNBR 680-AM host Brian Murphy.

York again refused to divulge details what led to Sunday’s so-called mutual parting with coach Jim Harbugh, but York did state that their differences were “football philosophy” rather than “personal philosophy.”

Echoing what he said in Monday’s press conference, York brought up how, “winning with class is what matters.” That sparked this dialogue:

Murphy: “Were you not winning with class?”

York: “Are you not going to blast us for off the field stuff for the last three or four years?

Murphy: “Was that Jim Harbaugh’s fault?”

York: “Collectively it was all of our fault.”

Murphy: “So why weren’t there more heads rolling other than Jim Harbaugh’s? Should Trent Baalke have been held accountable and maybe a mutual parting of ways with him?

York: “I mean, I think Trent and I are philosophically aligned on what we want to do with this team.”

Shortly after the 18-minute interview concluded, the 49ers’ Web site posted a 1-on-1, video interview York taped Monday with Ted Robinson, the team’s play-by-play voice. In that eight-minute session, York spoke about wanting to find a coach to emulate the late Bill Walsh, and York also invoked advice he received in the past from New England Patriots’ coach Bill Belichick about being a “hunted” franchise.

Here is a link to Murphy’s interview on KNBR..

Here is the transcript from Murphy’s interview with York:

Q: I’m going to ask you a lot of unpleasant questions because I don’t like the move. I’m a big opponent of the move. I think you guys are going to rue this move and I think this could be a negative turning point in franchise history. So, my first question to you is, I was stunned by this stat, there have been only two other times in the history of the league that coaches who have 44 wins in 4 years have left a team for a reason other than retirement. George Seifert was fired by the 49ers. Mike Holmgren left Green Bay for Seattle. So how can you justify a move that is at odds with the history of the NFL?

A: “It was mutual. This wasn’t just the 49ers’ decision.”

Q: Well, Jed, that’s a huge issue for me. Because Jim Harbaugh was asked on a number of occasions: what is going on with the story, why is this happening. And Jim’s specific words were: “I work at the pleasure of the organization.” So there’s a huge dichotomy between him saying “I work at the pleasure of the organization” and you saying it was “mutual.” Which is true?

A: “I mean, Jim said it was mutual at the end of his tenure with the 49ers.”

Q: He didn’t. In fact, his last press conference he said, “I work at the pleasure of the organization.”

A: “Was, did you not see the press release that Jim and I put out together?”

Q: I did, but it was at odds with what he said at the podium. So I’m trying to figure out which was true?

A: “I’ve had conversations with Jim. It was a mutual decision.”

Q: So you continue to say it was mutual. He says he wanted to work there as long as you guys would have him. That just doesn’t add up. Two plus two doesn’t equal four.

A: “You can ask Jim if you want. I mean, I sat down with him as we put together a press release. I mean, I don’t know what else to tell you.”

Q: “OK, well I guess we’re going to have to just leave this one hanging. That he said one thing, you said another and we’re just going to have to figure out who we believe. Cris Collinsworth said something in Week 1 that I just couldn’t let go of, and it’s just been nagging at me all year. And that is, he said, ‘The 49ers have a winning situation going on right now. And we hear there’s discord as early as Week 1. It is now the 49ers’ job to keep this together, because winning is hard in the NFL. And it is your job, Jed to manage the dysfunction or to manage whatever the philosophical differences were because winning is the only thing that matters and you guys were winning.’ Why couldn’t you manage it?

A: “Winning isn’t the only thing that matters. Winning with class is what matters.”

Q: Were you not winning with class?

A: Are you not going to blast us for off the field stuff for the last three or four years?

Q: Was that Jim Harbaugh’s fault?

A: “Collectively it was all of our fault.”

Q: So why weren’t there more heads rolling other than Jim Harbaugh’s? Should Trent Baalke have been held accountable and maybe a mutual parting of ways with him?

A: “I mean, I think Trent and I are philosophically aligned on what we want to do with this team.”

Q: So winning with class is a huge thing, you mentioned it yesterday, you mentioned it again today. So this is now maybe, we’re getting sort of closer to the smoking gun. This is a problem you had with the Harbaugh era?

A: “No, I mean, this isn’t on Jim, this is on the collective group of us. It’s equally on me, Jim and Trent.”

Q: So why was Jim the one to pay the price?

A: “He wasn’t the one to pay the price for that. This is just something we need to concentrate on and focus on as we move forward.”

Q: Man, I’m having trouble coming to grips with … somebody sent me, a listener sent me a quote from the Bill Walsh book, and I thought wow this is kind of stunning, Bill Walsh’s “To Build A Winning Team”: “The bottom line in professional sports is winning. Everything has to focus on that product: winning football games. Other offshoots mean little compared with being successful on the playing field.” That’s exactly what Bill Walsh wrote, the guy you cited in yesterday’s press conference. You guys were winning at a historic clip and you’ve chosen to go the other way. How can you justify that?

A: “I mean, you’ve asked me that like 17 times already. This was a mutual decision between Jim and I. I don’t know what else to tell you. If you refuse to believe that, I can’t help you. I don’t know what else to say. This wasn’t an easy decision for me. This wasn’t an easy decision for Jim.”

Q: OK, let’s talk about the other things we can answer and that is, there is no question, that there were leaks from the building. Because I don’t believe Jay Glazer, Trent Dilfer, Ian Rapoport, and Deion Sanders made things up out of their own head. Somewhere in your building, someone planted stories. Who was planting them?

A: “I have no idea.”

Q: Why didn’t you address or take issue with the leaks to stop them because it was showing to be counterproductive on the field.

A: “I don’t know that that’s the reason we were counterproductive on the field. I think you see a lot of distractions with buildings. You see a lot of distractions with teams. So I don’t believe what people are reporting necessarily reflects what you do on the field.”

Q: Well when you say winning with class, I don’t think a classy organization would allow that kind of subterfuge or sabotage to go on. Don’t you see that as at odds with winning with class?

A: “I do. And we talk about leaks all the time. It’s just not something that we tolerate. I’m not going to sit down, and you know … you can go through people’s emails, you can go through people’s text messages, that’s just not something I’m going to sit down and do. I don’t know where the leaks came from. I don’t speak to Jay Glazer. I don’t speak to Deion Sanders. I don’t speak to those people, so I don’t know where those leaks came from.”

Q: Was it important to you to cease them? When the first sort of red flag that went up, was it a priority for you to cease them, or was it not important and you just let it play out?

A: “To me I think it’s important that we focus on the field.”

Q: OK, and again we get back out on the field where you have a historic number of wins and you chose to somehow find philosophical differences, which is the phrase you kept using yesterday. And now can we, in a one-on-one situation, can you please enunciate, for all the, you guys talk about the faithful all the time, and you want the faithful to pay their tickets and go to your stadium, and the faithful have asked me a million times, what were the philosophical differences?

A: “Did you ask Jim what the philosophical differences were?”

Q: Jim said he worked at the pleasure of the organization. You’ve already somehow dismissed that so I can’t get anywhere with what you think about what Jim said. So I’m asking you: what were the philosophical differences?

A: “Jim and I had those conversations.”

Q: What were they?

A: ” Those are personal conversations. Those are not things we are going to talk about.”

Q: So was it football philosophy or personal philosophy?

A: “Football philosophy.”

Q: It was football philosophy. So does it get back to, like, how the offense was performing? Is that what you’re talking about?

A: “I told you, I’m not going to go into specific details. This isn’t personal. This isn’t about do I like somebody’s personality, do I not like somebody’s personality. I understand that there are high levels of tension when you get into sports. That’s absolutely par for the course, that’s what you deal with. I mean, what we’re trying to figure out is: how do we continue to improve, how do we continue to get better.”

Q: So you will continue going forward to refuse to enunciate the philosophical differences, leaving it behind closed doors. You do not want to address those specifically?

A: “I mean, I realize that’s a lame answer. I realize that that’s something that fans, they want every single detail. I understand that you want every single detail. But I respect the conversation that I had with Jim behind closed doors. I respect the fact that there are many people involved about those discussions, and not just those people but their families, and I am not going to throw those people under the bus. I’m not going to throw Jim under the bus. I respect him too much. I respect what he did for the San Francisco 49ers too much, to appease the crowd today, to talk about something that he and I said was going to stay behind closed doors.”

Q: Two things I think would dispute you not throwing Jim under the bus: the Thanksgiving night tweet was not something that I think something you should have addressed with your coach before you sent out. I think Jim probably felt blindsided by that and a lot of people saw that as throwing under the bus. And also, I think the constant leaks to Jay Glazer, Trent Dilfer, Deion Sanders and Ian Rapoport is throwing Jim under the bus. Would you not counter that?

A: “Listen, I didn’t leak anything to those people.”

Q: OK.

A: “Period.”

Q: Somebody did.

A: “I’m sure they did. I mean, that’s fine. You can suppose and guess on who that is. There are a lot of people that are connected to this organization that aren’t necessarily in this building. So you can start getting into leaks and figuring out who you think it was and what you think happened. But to me I think that’s counterproductive.”

Q: Did you throw Jim under the bus for that Thanksgiving night tweet? That was viewed as a serious power play in which you were definitely slapping the coach in the face who was tried to win a game and didn’t.

A: “How was that a power play?”

Q: Because you didn’t talk to the coach before you sent it out. It was almost like, I’m going to throw red meat to the masses while the coach is in there licking his wounds after a bad loss.

A: “I explained the tweet yesterday. When Lowell Cohn asked and he said his readership, you know, that was their No. 1 question to him. And I explained it. We had 70,000 people change their Thanksgiving plans to come here and we played well below our level. Period.”

Q: Do you think it would have been more appropriate to send it out after you talk to the coach and say, ‘Hey Jim, that was unacceptable and I’m going to tell the people that was unacceptable.’ I mean, you guys are in a professional business of high money, high stakes, big ego and a lot of respect and that came across as disrespectful. I guess you’re right, you did answer it yesterday, we should move on.

A: “That’s fine, I mean I can understand why you think it came across as disrespectful. That’s fine. I think it’s my responsibility to give our fans a product that I think is fulfilling of the San Francisco 49ers. And that night was not an acceptable performance.”

Q: No question, but I think, well, circling back, I think the last four years have been a very acceptable product that you guys have chosen willingly to dismiss.

A: “We have not chosen willingly to dismiss.”

Q: Yeah, you have.

A: “No we haven’t. We sat down together. We had philosophical differences. Jim has signed a contract today to be the head coach of the University of Michigan, a place that has been in his heart for a long time. He had a very difficult decision four years ago deciding between the 49ers and the University of Michigan.”

Q: Jim said he worked at the pleasure of the organization and people close to him have said he wanted to stay with the 49ers. And that is just the hanging issue in the air that I think fans, until you guys make a hire that goes and wins a Super Bowl, is going to hang over this team for a long time. It’s very, very frustrating.

A: “We have not won a Super Bowl yet, have we?”

Q: No you haven’t, and so that means you’ve had five successful seasons and 63 busts in the history of this franchise. That’s another thing I wanted to ask you about, is do you regret that comment yesterday about a Super Bowl is the only acceptable alternative. That seems wildly unrealistic and certainly creating a very difficult situation for your next coach to step in to.

A: “If a coach doesn’t understand that our standard is winning a Super Bowl, he’s not the right coach for the 49ers.”

Q: Everybody wants to win a Super Bowl, but it doesn’t happen every year. And are you not creating sort of a wildly unrealistic and almost silly standard there?

A: “OK, our standard will be, ‘Hey let’s just have a seven or eight wins season this year, you know. That’d be good.”

Q: No, standard could be the best team you could be and see what happens.

A: “Let’s win nine games next year because we only won eight games this year.”

Q: OK so you’re going to stand by that. So whoever your next coach is knows that a guy who went to three straight NFC championships and never had a losing season was not good enough. Your next coach has to understand that right?

A: “Listen, if we can replace Bill Walsh, who won three Super Bowls, and we can replace other people that haven’t won Super Bowls, I feel like we will continue to find people that understand the importance of being the head coach of the San Francisco 49ers and understand the standard that was set by Bill.”

Q: Couple of last questions Jed and I appreciate you sitting here and taking these questions. The big, big one is you kept saying over and over again: ‘Hold me accountable, hold me accountable, hold me accountable.’ And a lot of people asked me , and they were right, ‘How can we hold you accountable?’ Does that mean you refund PSLs, does that mean you give away beer for free, does that mean you resign? How can we, we can’t hold you accountable. What does that mean? Does that just mean verbal tongue lashings on the air? How can we hold you accountable in any meaningful way?

A: “I mean, you’re trying to give me a verbal tongue lashing now. And I mean I’m not sure what else to tell you on how to hold me accountable.”

Q: Well, you said you want to be held accountable. So we’re wondering how can, people were actually saying, ‘I’m a season ticket holder, and I want to know, how can I hold him accountable?’

A: “I’d love to hear from fans. I’d love to hear from them. And if you have suggestions for me, if you have thoughts about what we can do better, and if you think we’re not performing to a level, you can let me know. And you can decide the best form that you can communication that with me.”

Q: OK, last couple questions for you Jed. Is that a lot of people including me, and I’ve thought this a lot, you guys are missing a John McVay, a Carmen Policy. I understand Paraag Marthe is a very bright guy. I know him, and you guys got the stadium built. I understand Trent Baalke is a great football man. There needs to be a, in my opinion, there needs to be a wiser, an elder voice in there, not unlike what the warriors did in bringing in Jerry West. John McVay was that man. Carmen Policy was that man. Would you consider adding another voice that has a lot of league experience, so that situations like what just happened –a very successful and winning coach was not able to be managed in a proper way, a situation was able to be managed in a proper way — would you add an elder statesman who could manage these situations in the future?

A: “We’ll do anything to help this team get better and to win.”

Q: So does that mean you’ll do that?

A: “We’ll do anything to help this team to get better and to win.”

Q: I would recommend it. That’s just from me. One guy who sit here, and I covered the team for years as a beat guy. And it helps to have cooler heads because I circle back to kind of my original statement, which is I felt it was your job, as the elder statesman there, you were the guy, to manage the dysfunction between Trent and Jim.

A: ‘And that’s again, did Jim say that there was dysfunction between he and Trent?”

Q: Well no, I only learned that from all of the leaks that came from the building.

A: “But did Jim say that?”

Q: No, Jim said he worked at the pleasure of the organization.

A: “Right, but at the end, at his final press conference, what did Jim say about his relationship with Trent?”

Q: Well, I don’t remember the exact specific quote, but I can tell you that he wanted to stay. From my understanding he wanted to stay. And you’re saying he didn’t.

A: “Then I would assume if he wanted to stay, that he had a pretty decent relationship with Trent. Is that correct?”

Q: Well, apparently the situation was managed to the point that he’s no longer the coach, so it was not managed properly. So I think that’s what we’re left with and I think that’s what we, we started the season this way, we end the season this way. And listen, Jed, I said it before: you guys have a chance. To me the analogy is the ball is on your own 1. You guys are going to have to drive 99 yards now. You can score a touchdown, you can hire a guy who will fix this team, but you guys have put yourself in a difficult situation because you had a winning coach, and you’ve now dismissed it. I would add, and it’s not encouraging to me, that this is the second time in the York ownership that you guys have dismissed a popular and winning coach for no apparent, good reason. You know what I’m saying?

A: “I hear you. And, you know what, nothing that I say is going to appease you. The only thing that is going to appease you is doing exactly what you just said: bringing the right person in here, and getting the team back to a Super Bowl-winning caliber. Period.”

Q: That’s it. We’ve covered the ground. And I appreciate you putting up with a vaguely hostile line of questioning.”

A: “Thank you. It’s always a pleasure.”

For more on the 49ers, see Cam Inman’s Hot Read blog at blogs.mercurynews.com/49ers. Follow him on Twitter at twitter.com/CamInman.