I have been doing a motor swap in my 94 Z28. I found a 96 motor from a wrecked camaro. I replaced the motor and now I have a weired issue. The flywheel looked worped while spinning on the motor. I bought a new flywheel and the same thing. The flywheel spins like its worped. I know that it cant be worped because it is brand new out of the box. Would the flywheel do this with out a trans hooked to it. Please guys I need alot of help with this one.

Thanks

 

Sounds like the crank flange is bent. Take the flywheel off and check the runout on the crank flange (and make sure it's just not some gunk on the mounting surface).

 

I did replace the rear main, would that have something to do with this?

 

No replacing the rear main seal shouldn't affect it. As shoebox suggested, check the crank flange for a bend in it and check that you don't have a bunch of crap between the flange and the flywheel.