Can you show a couple more pictures in the rear? In particular where the ambulance door jam meets the sill at the bottom and where it meets the mid bar (above the lower quarter panel). The front of the new quarter panel appears to be meeting the rocker panel at the correct spot....but did the rocker panel get replaced (seems a bit tall)? If the bed did not get replaced ...nor the wheel wells then the top of the sill should be perfectly level front to back with the ribbed bed.
That curve bend and the lower quarter panel bottom is a bit nebulous (imprecise). It would be better to measure from the tub top in an exact location such as
where the sill meets the quarter panel. I can get you that measurement but a picture around the sill can tell me a few things.
Also your weather stripping is pinching and perhaps holding off the upper quarter from tightening down fully. That can throw off the opening size.