Well Nova 1958, by your last post I can tell you are a patient man and I thank you for that. I looked at your link and it seems to me that "69LT1Nova" gave you good advice there...You should be able to get a fit and finish of gaps and alignment that you may be able to live with. Follow what MARTINSR. just suggested, you can never cross measure enough from constant points...Please understand that anyone who has posted here has only had your best interest at heart and we are trying to help you with the information we are given...I understand that it would take you days to type everything you have done to the car.
You may need to get your front sub-frame square to the body and not the rear frame rails, correct me if I'm wrong Brian , but, the rear rails being what they are and where they are they aren't moving. If you follow all procedures that GM used with jigs and locator pins your car will not come together the way it looked in 1972 when it rolled off the assembly line...even GM used the locator pins as a guide and not a do all end all, but, they where working with new undamaged frame and body components.
Again, follow what Brian has posted and God willing you will get closer to a satisfactory fit for your Nova. Building a car from the frame up should be just that, starting with the frame and moving upwards, just like building a house. I currently have several projects for customers, one is a 1930 Model A 4 door and am converting it into a 1/4 ton truck. This involved cutting the back half of the car off, removing the rear doors section and welding the remaining back of the car to the front giving the vehicle a cab. The first thing that needed to be done was to get the frame and all mounting points in there proper place with numerous mock ups. Then I began the reassembly process, taking many measurements along the way...on a uni-body such as your Nova it's even more important as your not working with a full frame.
I thank you for your patience, I don't know if I've helped at all and do understand what you are going through. The hardest thing to fix is the thing that somebody else already has tried to fix. Please keep us informed, I'm learning as well and I sincerely wish you success in this project.
Best to you.