For the past couple of years, BART hammered home the message that the system was aging and overcrowded and needed to be rebuilt. Voters listened and approved a $3.5 billion bond measure last fall.

So now the transit agency, its leaders and riders can breathe easy. Not so fast.

Despite the now-funded plans to rehabilitate the train system with the money from Measure RR, delays and breakdowns will probably continue — and, as BART officials acknowledge, things could get worse before they get better.

It will be at least two years before riders begin seeing significant improvements from new rail cars and system fixes paid for by the bond measure money. In the meantime, declining revenue and rising costs mean BART could face a $25 million to $45 million operating deficit in the coming budget year.

The news comes in the shadow of a frustrating few months marked by increasing delays and major breakdowns, including a Jan. 6 incident in which a train stalled and locked up near the West Oakland Station and couldn’t be moved for more than an hour at the peak of the commute.

It’s too early to tell what the looming budget gap will mean for riders, but the possibilities for covering the shortfall range from service cuts and dirtier trains and stations to more advertising, allowing corporations to pay to have their names associated with stations, and making changes to fares and parking fees that could leave some riders paying more.

Grace Crunican, BART’s general manager, said the projected shortfall in the district’s approximately $800 million budget is not an emergency but needs to be dealt with.

“This is not ‘red flag! red flag!’” she said. “This is a chance for us to get out in front of it, to adjust.”

The budget shortfall, and possible ways to deal with it, were among the topics of an informal but wide-ranging discussion recently by BART directors and key officials meeting in a Berkeley hotel ballroom.

With the bond measure passed and three new members on the board, Crunican said, it is time to refocus on issues BART has largely ignored for four years.

They include how BART should handle its perpetual parking shortage, how fares should be calculated and charged, how much advertising is appropriate and whether corporate names should have a home at BART stations.

“We’ve been so hellbent on getting the system fixed,” Crunican said. “This is a chance to look at everything else.”

BART staffers examined the system’s policies for fares, parking and advertising and then came up with a menu of possible changes that could help directors balance the upcoming budget. No decisions have been made, but some of the ideas are likely to come up for discussion as budget talks progress.

Wrapping more trains in colorful advertising and covering station walls, ceilings and floors could bring in millions, said Aaron Weinstein, BART’s chief marketing officer. So could sprawling video displays. But they could also irritate passengers, new director Lateefah Simon of San Francisco said.

“I’m all for it,” Simon said. “But how do we do it so BART stations don’t start looking like Target?”

BART could also sell a form of naming rights that would allow stations to keep their current names while attaching the name of a nearby business. For example, the Powell Street Station could have a sign beneath its name reading “Home of Westfield San Francisco Centre” with passengers on approaching trains hearing the announcement “Next station: Powell, home of Westfield San Francisco Centre.”

Stations could also become the home of technological displays such as charging stations or video information screens that would, of course, prominently feature the names and emblems of their sponsors.

BART officials say they have no plans to sell station names outright, preferring not to disrupt the familiarity of the system and risk having to change names every time a sponsor changes its name, Weinstein said. They are also well aware that such a proposal would generate controversy.

Fares are also being eyed, but not necessarily for the typical across-the-board increases. Instead, directors could consider charging higher fares during peak hours in peak directions or assessing a surcharge for riders who use magnetic-stripe tickets instead of Clipper Cards. They could also raise the $1.95 minimum fare to match those of local transit agencies like Muni or AC Transit.

Directors also urged a crackdown on fare evasion, which Crunican said is in the works. BART does not have a detailed estimate on how much it loses to fare cheats but says scofflaws cost the system millions of dollars annually.

BART’s oversubscribed parking lots could also raise money through a variety of changes. Among the options being looked at are providing more spaces for monthly permits; raising the maximum daily fee on spaces; charging fees that vary by time of day and day of the week depending on demand; selling access to premium reserved spots; and offering valet parking. Such approaches could raise money and help BART better manage its parking shortage, said Bob Franklin, BART’s accessibility manager.

As officials consider new sources of money to operate BART, systemwide rebuilding efforts, to be paid for with the Measure RR money, are beginning. The run-up to selling bonds has started, and BART is developing hiring plans, designing improvements and starting studies, all things required before construction can begin.

But some of the work on BART’s most critical needs is nearly ready to go and will start this year, said Tamar Allen, BART’s chief maintenance and engineering officer.

Ten miles of track and two crossing tracks will be replaced along with worn power cables in three Oakland locations and power substations at the eastern end of the Transbay Tube and in San Leandro. Three waterproof substation roofs will be built and canopies will be installed over escalators at Powell and Civic Center stations.

“This is really exciting that we’re getting going so quickly on this,” said Nick Josefowitz, a San Francisco director. “I’m already getting emails from people saying, ‘I voted for the bond, why aren’t things better already?’”

Help is on the way, Crunican said, but BART riders will have to be patient. Much of the relief will come with the arrival of the new rail cars. BART has ordered 775 new cars, and the first 10 are being tested, running on different lines in the early morning darkness before the system opens for the day.

BART officials won’t say when, but someday soon those cars will start carrying passengers. If all goes smoothly, BART will tell manufacturer Bombardier to crank up the assembly line for the rest of the order. Once it does, BART expects 16 new cars will arrive each month.

Michael Cabanatuan is a San Francisco Chronicle staff writer. Email: mcabanatuan@sfchronicle.com Twitter: @ctuan