question about the flywheel and converter

Well I just bought a 00 xj and the motor was blown so I bought one from a salvage yard out of the same year and when I put it in the is a shake. The other day I unbolted the torque converter to see if it was in the motor and there was nothing so I rebolted the converter and the shake was back so then I unbolted it and tried every position.So tonight I took the trans out to see if any weights came off the converter and everything seems fine so I looked at the old motor and flywheel and noticed that that flywheel has 9 extra holes drilled in it while the one on the new motor only has one. My question is are the converter and flywheel matched. I swapped the flywheels but not sure if that is going to solve my problem. Hopefully some one on this forum can help cause this jeep is a gift to my wife and I was hopeing to have it donein the next few days. Thanks for your time.

1. Flywheel = clutch and manual transmission.

2. Flexplate or drive plate = automatic transmission.

3. No, not matched to the engine.

4. Make sure you didn't tweak the flexplate during the engine install. Were you naughty and attach the torque converter to the flexplate and then jam that into the transmission? If you did that you most likely damaged the torque converter or the pump and seal at the front of the transmission.