No museum in its right corporate mind would attempt to build an operating 3rd-rail line, BART-gauge or otherwise. It's just impractical. Look Back East - does anybody have operating LIRR equipment in a museum?

Plus, if you really want to operate it at speed, you would need some miles of track - much like the test track when BART started, between Concord and Pleasant Hill - and at modern prices, even if the land were free, would need a budget in the high hundreds of millions. Sure, you could save some money because the train control system would only be running one train not integrating it with the rest of the system, and the stations could be much simplified (no architectural concrete masterpieces needed) but still, at best, it would keep the budget under a $billion. It's on the order of a Bill Gates project not something you would get ordinary donations for. Then, think of the maintenance and security and the fact that even if you built 3-rail track and overhead wire the only other equipment you could run would have to be high-platform boarding; it would have to be completely separate from anything else a museum is doing. Again, a Bill Gates-scale endowment would be necessary to take care of it.

So: stuffed & mounted is what you get; that can be done by an ordinary museum (say, Niles Canyon or CSRM). Would also say Rio Vista but they seem to have too many internal problems to put together something like a BART car exhibit - you'd probably see one trucked to OERM before Rio Vista could do something.

Realistically, assuming they're aluminum, retired BART cars are most likely, like old airplanes, to become beer cans.