Alright, can't put this off any longer. The fit all across the back is as near perfect as I could hope for.
Fit on the passenger side is good enough to seal with the bulb seal.
However, (and I knew this) the fit on the driver side was just terrible, with a gap of at least 3/4 inch in places. Time to bend the fiberglass. Found a 4x4 and cut it to the contour of the bottom of the top as was.
Then scribed and did a matching angle cut to fit the pieces inside and outside the top at the flange.
Probably spent an hour with the belt sander getting the fit just about exact and then clamped everything up. Cut some small wedges to insert under the lip and started heating the lip of the top to about 375 degrees F. Worked it up and inserted the wedges, heated some more, wedges in further, until I had moved it about 3/4 inch where it needed to be.
Left it sit overnight and next morning the fit to the body was, while not perfect, certainly good enough for the seal to work properly