For what it is worth, in the 70's parts from the Ford factory had many variations in them as well. Tools break, they get fixed, they get made from scratch midway through a run. Variance in the sheet metal width can also affect the panels...every little bit of variation adds up in the end.
Example. Next auto show, measure the hood/trunk/door width of all the Mustangs you see. Compare your numbers. You will probably be off by 1/8 of an inch. That is quite a bit when trying to get panels to line up.
I may suggest when looking for ANY part, new or used, take measurements of the dimemsions that are critical to you, and assure the parts you buy have similar dimensions. If you are looking for a hood, measure the 2 diagonals. If they match, you need a square hood. If they don't match, you need a lopsided hood. Same thing with doors and trunk. Not sure how to measure quarter panels.
No easy fix here.