by "pads" in the flywheel i guess you mean the magnets..
The flywheel should have zero freeplay up, down, in, out or sideways..
Running it with a lot of engine noise may have been a bad idea. You may have bad crankshaft main bearings. However it may only be a loose flywheel. That can cause both poor running (timing is suffering) and noise.
Check see exactly what is loose.. the flywheel or the flywheel shaft itself.