Some Trump campaign associates have sent letters to the Justice Department’s special Trump-Russia investigator, complaining about how former special counsel Robert Mueller and the FBI conducted the nearly three-year investigation.

The letters were sent to John Durham, the U.S. attorney for Connecticut. Attorney General William P. Barr assigned him to probe how the FBI began its investigation into Donald Trump’s 2016 presidential campaign and whether there was improper surveillance.

J.D. Gordon, a former Pentagon spokesman and campaign national security adviser, said his letter asked Mr. Durham to broaden his investigation into how Mr. Mueller and his team of mostly Democratic Party-aligned prosecutors conducted their inquiry.

“Trump-Russia was far worse than a simple hoax and political dirty trick,” Mr. Gordon told The Washington Times. “At the core, it was a crime wave waged against President Trump and dozens of his associates who were victimized by years of criminal leaks, violations of the Privacy Act of 1974 and various defamation laws.”

Trump supporters are particularly upset that Mr. Mueller’s 448-page report included the names of advisers, such as Mr. Gordon, and their actions when none was charged criminally. Federal prosecutors typically don’t provide narratives on unindicted people.

In Mr. Gordon’s case, at a 2016 pre-convention platform drafting in Cleveland, he edited a proposed amendment from a single delegate. He changed the language from promising lethal weapons to Ukraine to committing to all appropriate aid to the country’s military.

For that seemingly routine campaign act, he found himself under intense media, congressional and FBI scrutiny for more than two years.

“President Trump and associates were treated by investigators and their collaborators in the mainstream media as if we had no rights at all,” Mr. Gordon said. “It was always the presumption of guilt, not unlike the Salem witch trials of the 17th century.”

Mr. Barr hasn’t signaled that he wants a review of the 22-month Mueller investigation, which involved 40 FBI agents, 19 prosecutors and various intelligence assets.

The attorney general has said Mr. Dunham will review the use of FBI informants and wiretaps under the Foreign Intelligence Surveillance Act (FISA).

At least one yearlong wiretap is known to have been placed on Carter Page, a campaign adviser. At least two FBI informants were assigned to interact with another adviser, George Papadopoulos.

In a second letter to Mr. Durham in May, Michael Caputo, a campaign media adviser, raised questions about a man he believes was an FBI informant who contacted him in 2016 with supposed dirt on Democratic presidential candidate Hillary Clinton. The man is a Florida-based Russian, Henry Oknyansky, also known as Henry Greenberg.

Mr. Caputo would like Mr. Durham to determine whether Mr. Greenberg was, in fact, an FBI plant.

Mr. Caputo wrote his letters to Justice Department Inspector General Michael Horowitz and John W. Huber, the U.S. attorney in Utah who worked with the inspector general.

Mr. Caputo told The Times he received no response from either official. He then sent his packet of information to Mr. Durham, whose office confirmed its receipt.

“We sent the same letter to him with the same amount of evidence,” Mr. Caputo said.

The issue he raises is one focus of the Durham investigation: how many FBI informants were deployed against Trump associates and what they did.

It is known that two informants, Washington scholar and Cambridge University professor Stefan Halper and a female assistant, were assigned to engage volunteer Papadopoulos. Mr. Halper also made contact with Mr. Page.

The FBI placed a year’s worth of wiretaps on Mr. Page in 2016 and 2017 but never charged him with conspiracy.

Mr. Caputo’s gripe is that Mr. Mueller talks about Mr. Greenberg in his report but never addresses the fact that he was a longtime FBI informant. Mr. Caputo hired a private investigator who he says confirmed that fact.

Mr. Caputo said the Mueller report also suggests he attended a meeting with Mr. Greenberg when, he says, “they had incontrovertible evidence I wasn’t there.”

Mr. Greenberg’s supposed information on Mrs. Clinton never materialized.

Rep. Devin Nunes of California, the ranking Republican on the House Permanent Select Committee on Intelligence, also wants someone to investigate the Mueller team.

For one, he told Fox News, the special counsel’s office objected to his committee’s viewing of transcripts. He didn’t identify the transcripts, but the FBI or informants apparently recorded conversations with Trump aides.

“Somebody needs to look at these characters that were on Mueller’s team,” he said. “I think they obstructed justice. They obstructed a congressional investigation.”

Mr. Nunes, who pressed Democrats through bank subpoenas to admit they funded the discredited anti-Trump dossier sourced to the Kremlin, also said someone needs to find out what the FBI was doing in 2016 before the investigation was officially opened on July 31.

He referred to July 31 as a “paperwork” start but not the investigation’s real beginning.

“We know the FBI is involved to some degree,” he said. “We don’t know exactly what they were doing before July 31, 2016. Why? Because they wouldn’t answer the questions that we had over the last two years.”

The FBI began receiving material in early July from dossier writer Christopher Steele, a former British spy paid by Democrats. His numerous conspiracy allegations were either disproved or not substantiated by Mr. Mueller.

Republicans considered the dossier a Democratic hoax and possibly disinformation from the Kremlin figures who fed it.

Mr. Page was invited by an organizer to attend a conference at Cambridge University weeks before July 31. There he met Mr. Halper, the FBI informant.

The biggest question for Trump backers is: who is Joseph Mifsud, a London-based Maltese professor? He is the person who said the words that started the Trump investigation by telling Papadopoulos that he heard in Moscow that the Kremlin owned dirt on Mrs. Clinton.

The Mueller report profiles Mr. Mifsud as being exclusively Russia-connected and ignores all of his contacts with Western governments, including Washington.

Republicans wonder whether the entire three-year Trump-Russia saga was ignited by a Western informant, Mr. Mifsud. He has remained out of sight and not spoken publicly.

“It really appears like they were spying on the Trump campaign,” Mr. Nunes said.

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