At this point it might make more sense to rip out the old electronics and convert the model to Protosound 3. That way it will retain a lot of the lighting functions, have a much more realistic sound system, and have speed control.
But after looking at the model, the speaker and the couplers are a bit of a problem area. But in theory, they might work if they are the same resistance as the MTH parts.
There is one video online of an Atlas O Amtrak Dash 8 converted to Protosound 2. So that's some reassurance I guess...