"* Some how I put the pressure plate on in the wrong orientation, and the CPS is seeing the position of the crank incorrectly. But, isn't there only one way to bolt the flywheel up, otherwise the holes don't line up?"

Not the pressure plate, but the flywheel can be put on 7 different wrong ways. Ted has the answer for how it needs to be: with the crank at #1 TDC the missing holes are at the starter opening. I don't guess you got a Rex flywheel (the 40-hole variety) because as little as I know about 7/9 cars (those with Rex/Regina) I think they did not have M47's in US of A.

"* Bumped the CPS when installing the flywheel and damaged it or pushed it too far from the flywheel. But same issue as above, either it sees the flywheel or it doesn't, right?"

The bracket would be bent and probably fractured if you did that. But it is a mistake to think that sensor "works or doesn't."
--
Art Benstein near Baltimore

Back in the 1800's the Tate's Watch Company of Massachusetts wanted to produce other products, and since they already made the cases for watches, they used them to produce compasses. The new compasses were so bad that people often ended up in Canada or Mexico rather than California . This, of course, is the origin of the expression,..."He who has a Tate's is lost!"