If the door gaps to the rocker and quarter are good then the fender gaps are due to the subframe and/or core support bushings imho. Shimming will likely be needed.
Urethane wave needs to be blocked out with long stiff blocks and will remove a lot of clear. If you hit the base it’s game over and the panel needs to be repainted imho...
If you are also welding up emblem holes you are most likely looking at a complete do over imho...
Don
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