My best guess is yes they will fit the frame and swingarm will mate up all the same. However, the internals have me worried. If yours has a catastrophic failure you will essentially be buying a whole new transmission anyway, so shouldn't be an issue as far as generational crossover is concerned.
Still sounds like a recipe for a massive headache in the event you are forced to track down weird little problems trying to get it to work. I think it would be cheaper to buy a used EC 300 motor and going through it.
Look forward to seeing pictures once you split that case.
