Hi Mario,
Thanks for the info. I did replace the rails, and they measure out square and level to the ground at the same height. I'm in VA and don't have ready access to a frame bench. The issue can be in wheel wells as they aren't yet perfect to the quarters. Also, Mike from MCC pointed out that the weather strip gutter on the tailpan may need to be bent down and indeed it is off on the pass side. Not sure how far down to bend it. The deck is not perfectly flush the quarters, it rises up a little, as if it has slightly more curve to it.
As far as the datum points on the frame rails, that is a good point since I got this car with the back end all cut up, so I'm basically guessing where the frame rails, quarters, trunk floor, and wheel wells all go in relation to one another.
A big issue I have is the deck lid is coming in contact with the pass quarter where the bump stop would be installed. Not sure where the problem is but I have the original deck lid and I'm going to try that asap. Hopefully that will also solve some of wide gap issues too. Sorry to ramble on...
Ron