Snocross2xtremes is doing something like this with a 360/318 swap and he ran into flywheel issues. We were discussing it on Pirate for a bit. I don't know what tranny you have since you did not identify a tranny in your "tranny question" and you asked if the motors will swap in place of each other, but if there are different flywheels, you may find that there are different flexplates and/or convertors.
I would PM Snocross and ask him what he was doing to see if its applicable to what you're doing. He may have some useful info for you.