I'm thinking about buying an fc with a bad motor, it has a 5 speed. I have a good motor that came from a car with an auto tranny. What's involved? I'm thinking; at least the fly wheel would have to be changed? TIA

 

I'm probably wrong I've only done it on an FD.
You'll end up having to change your driveshaft and diff since they connect differently.

 

If you're keeping the existing drivetrain, the engines themselves aren't any different. If they're different series motors then you'll run into problems because the counterweights changed, but other than that, the only difference is the manual car uses a weighted flywheel with a clutch - the auto car uses a counterweight with a pressureplate and torque converter. Either way they bolt on the same way, and the engine is the same.