Some semi-historical ramblings - - -
Wish I could be of more help, Bill, but my information is VERY limited, and is only typical of the "normal" Super .38 of whatever time period.
First, I have no information that the FBI ("Division of Investigation," I believe, early on) ever actually issued Super .38s. Not saying they didn't, only that I don't have any printed information. In the early days, they could carry pretty much whatever they wanted, so long as they could get the firearms training guys to approve it. I wouldn't be a bit surprised to learn that the Bureau got a purchase order and had Colt's ship them a bunch of Supers, for anti-vehicular use.
I read somewhere that the famous agent, Melvin Horace Purvis (The Man Who Got John Dillinger!) committed suicide in 1960, using an engraved Super .38, but, of course, this would have been a personally owned pistol. I did a Yahoo! search on Purvis today and read through most of the FBI file on Purvis, furnished as result of a Freedom of Information Act query. At least three references are made to a .45 Colt automatic with which Purvis ended his life. In fairness, there is some question as to whether the death-by-gunshot was an accident. One account is that the .45 was a gift from fellow agents when Purvis resigned from the Bureau in 1935.
Another point, though - - Since the Super .38 and the .45 Government Model were practically identical, it is quite possible that someone might see the pistol at the scene, or in a death scene photograph, and merely (and pretty logically) assume it was a .45. For years, it was taken for granted that Captain Frank Hamer had carried a .45 on the Bonnie & Clyde ambush. Turns out it was a Super .38 which Hamer had procured especially for that job of work.
Back to your questions: Since the Super .38 was introduced in 1928, all of them would have been built on the 1911A1 type frame. This would indicate arched mainspring housings, long tang grip safeties, short, broad hammers, and short triggers. As mentioned above, the individual users might well have substituted 1911-era parts to suit their own tastes. I've never heard of special stock panels being supplied, but, again, the individual might have installed his own.
Colt's marketed a pistol called the Super Match, which was a Super fitted with slightly higher, adjustable rear sight and corresponding front sight. It had a dream trigger, specially fitted and honed to a "glass rod" break. As there were some very proficient shooters in the Bureau, I'd be surprised if at least one or two Super Match pistols weren't carried by working agents.
I've never seen an authenticated FBI handgun with special markings - - But then, I've only seen six or eight. All the S&W M&Ps and Model 13s, and old Colt OPs were standard commercial handguns. S&W presented FBI Director J. Edgar Hoover either the first, or one of the very first, .357 Magnums. There were a lot of 3-1/2 inch .357s carried by agents, early on.
I fear you'll have a difficult time replicating "an FBI Super .38" and making it a very "special" piece, Bill. Any pre-WWII Super could serve as a representative example. I say pre-war, because the .357 was not introduced until 1935, and they were in pretty short supply until after WWII. Therefore, a Super .38 would have been a very valid choice for an agent's sidearm from 1928, well into the late 1940s.
I regret that I don't have any references which tell when the Bureau began requiring agents to carry issue handguns.
Again, good luck on your project.
Best,
Johnny