This is the biggest fit problem on this door and not surprisingly, it's where the replacement cowl is. The gap is wider at the top than at the bottom. Probably the easiest way to fix this will be to smooth out the door opening and build up the edge of the door and shape to get an even gap. This is close enough to fix without resorting to cutting and beating the cowl.

LATER EDIT: After getting an expert opinion I re-fit the outer cowl to close the gap. All that was necessary was to make a single cut where the panel was hitting the upper cowl preventing it from moving aft to close the gap. With the door fit properly everywhere else I just fir the outer cowl to get an even gap. All things considered it is a much better fit with less work.

The bottom contour where the cowl and door wrap under will need a little reshaping, but all-in-all I'm very happy with the way things fit.