1st, welcome to TC! Nice ride.
Regarding the last post and the right fender alignment, I can also see in the photo that the front edge of the door is exposed/visible. The rear edge of the fender is supposed to be out just a bit relative to the front edge of the door, for aero purposes and also to allow the gap to be closer without knocking off the paint on the peak of the door.
Do you have a copy of the 69 AIM? If you have concerns about the gaps and the way the wheel sits fore/aft in the opening, the best way to begin would be to start checking how the front sheetmetal is installed relative to the way the factory did it. Need to look at door to fender gaps, squareness of the assembled pieces (cross/x measurements across the fender edges with the hood up, etc), and so on. If you do not have the 69 AIM, PM me and I will get you one.
It can be a pain, depending on how bad things are misaligned, how much (like say, the hood) has to be removed to allow proper adjustments, and whether reproduction sheet metal has been installed and what the quality of those parts are. But with the factory procedures and data/measurements, you at least have a road map.
It is also possible, in addition to sheet metal adjustments, that you need to look at the subframe bushings, bushing mounting points (common rust area, allows subframe to move in ways GM did not intend), and subframe alignment (more measuring fore and aft, and cross dimensions from specific reference points to make sure the subframe itself is aligned correctly. That info is in threads here I can steer you too, and/or send you some parts of the 69 Fisher Body Manual.
It's always something