I was wondering if anyone could tell me how (save the physics) using an 88 or earlier flywheel could throw off the balance of an 89 or later motor... plus could anyone fill me in on the trans mount mods to a switch a ninety one auto to 5spd

 

The S5 rotors are lighter than the S4 ones. Without the physics, that's all you're getting!

When you swap gearboxes, you use the gearbox crossmember that goes with the gearbox you're installing.

 

okay lets stab at this, flywheel completely balanced, all 360 degrees of it, the question must come to the counterweight, does the counterweight not bolt up to the older flywheel,
I also heard that an auto floor pan did not take a five spd "crossmember"
help me

 

It's the fact that it's not perfectly balanced to the weight of the rotors. It'll vibrate a little at low RPM and then at high RPM but in the end it's bad for your motor. If you don't care then go ahead. I believe the holes for the manual crossmembers should be there. even though you have an auto.