I had to put a different transaxel in this ZX2. Now it is making a knocking noise. I pulled the cover off to check the 4 nuts on the flywheel. It looks like something is rubbing on the flywheel (it's just a bit thicker metal around each of the nuts). Any idea what could have moved? The flywheel couldn't have moved toward the block, could it? Maybe the metal plate between the block and trans? Any ideas before I take the whole thing apart would be appreciated.

what do you mean by "different"

Used one out of a wreck. Same type. Sorry about the confusion. It sounds like the noise is coming from the flywheel. Trany shifts fine.