Wow, can't quite figure out from what you said what engine is where and what flywheel came from what.

It sounds like a major head-ache if both engines weren't put at TDC and marked on the flywheels and crankshafts before disassembly.

With some expertise and know-how, you could figure this all out. I haven't seen these flywheels for awhile and so can't give you any pointers other than try to figure it out before re-installation. Don't know if the engine you got was pulled complete with fuel rails, manifold, etc, but if so, there should be a way for you to rig it up and start it out of the car so you can be sure you put it all back together correctly before install.

Hope someone pitches in and gives you some info...

Good Luck