Dog,
The Ford transmissions were more popular back then because of their higher strength (high nickel gears, etc.) The Pontiacs even ran Ford Transmissions. Nascar's only rule was that it had to be a standard trans.
I don't know who owns that engine assembly that is in the Petersen Museum but my guess is that is came from one of Smokey's auctions along with the trans. The front case is probably a GM case so it will bolt up to the Chevy bell. (or they may have just modified the Chevy bell, but I doubt it).
I don't know who put that assembly together for display. It could even be a 3-spd. After all, they weren't drag racing... 3-spds were used a lot in those big cars.
Verne