As far as the flatness of panels across the gaps, it would be difficult to work the fenders with hammer and dolly, due to the fact, there is inner structure behind the outer panel. I have clear areas that are low, you can feel with your hand, and see from block sanding. Towards the top of the fender at the door, the fender is lower than the door and an area, on fender, that is clearly lower.
The same goes for my door. The door cannot get aligned any better than it is now. Body lines match up perfectly. The door gap has issues, but that can be easily addressed with a little work. However, at the door handle to the top of the door, the door is sunk in more than the quarter. This leaves a mismatch with the flatness of the panels across the gap. I have moderately block sanded this area and it has revealed to be low in this area. Also, in an effort to make sure the door is fit perfectly, the door is slightly lower than the quarter. In my quest for perfection, as I'm a perfectionist, I will have to address this. I have not given a great deal of thought as to the best way to fix this problem because it arose just yesterday after working on the door fitment.
Onto the fender to rocker fitment...The outer edge, where the fender folds over at the rocker and door gap, has never been disturbed. The patch that was installed did not disturb any of the original panel in that area. It was simply done on the flat area of the fender. The patch was done well, but quite some time ago. I can barely remember the time that I had it done. I did not do this patch. This is the one area of the car that I did not work on. I originally was going to farm out all the metal work till I got screwed over...Another story though...As I had originally shown in the beginning of this thread, The fender did not follow the angles of the door and rocker in that area. Yesterday, in a desperate attempt, I did some tweaking to that area of the fender to match the contours of the adjacent panels. I did succeed in creating a match, but now I opened another can of worms. I bent the fender in this area and now this lower section is not flat or have a gentle, slight curve to it. I created a bow in the fender, in which now, I'm afraid I'll have to reverse and do as you suggested. Your suggestion is probably the only proper way to do it and I'm not about doing hack work. I'm just highly frustrated at having such a difficult time trying to align original GM fenders, doors and rockers!