I have a very similar gap issue except mine is due to the top not being able to be any further forward because the A pillar bolts are all the way forward. See photos. I just decided to roll with it for now and maybe turn it into a future project. :)
Other things I've done to get "acceptable" body fitment is cutting off a small part of the front radiator frame to allow the nose to sit straight, I ended up having to raise one of the rear fenders 1/4" and I've also pulled the rear fenders in as much as I could to get decent gaps with the hardtop. Had to really push them in a lot and the gaps still aren't perfect. One side is pretty nice, the other so-so.
As for grinding down the rear hatch flange, I didn't have to grind anything but the corners where the intercooler vents are were the tightest (like your photo shows). I did have to grind the door flanges down entirely for the flocked weatherstrip to fit.
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