Not all '91s are a snap ring issue. You need the transmission number to know for sure. The wheels are a personal opinion and the upgrade is likely not an issue. The originals are pretty readily available. (I have a set in my garage though the car is gone.) As to the panel alignments, that could be reason for concern and someone with experience should look at it for you if that is not an area of expertise. The lower lip is often subjected to scraping if ground clearance in and out of driveways creates it, as it was with mine (no lip when I purchased the car and I had to learn the right angle to enter and exit the driveway once I added one.)
It might be time to lay eyes on the car and to go with someone with some additional NSX knowledge.