But is this a problem that can account of the day-to-day difficulties of managing and using BART? Yes, procuring new train cars is more difficult (and likely more expensive), but BART has lots of other problems to tackle.

The problem isn't just the rolling stock. Everything in BART is at least somewhat custom including control systems and software. Very little can be shared with public transit systems in other metro areas so there are no economies of scale. Thus BART has to do a lot in house or depend on a limited set of specialized vendors at great expense.

If you had to buy a special car to be allowed to drive on Bay Area roads because they weren't the same as the roads in Chicago or Boston then a Honda Civic would cost $1M.

  then a Honda Civic would cost $1M.

For $1M you could build a single San Francisco Cable Car. Plus it's built locally.

A cable car is a lot simpler than a civic - the complex parts are in the engine house elsewhere. the cable car is bigger but it has no engine, transmission and other such parts