Went out to the shop, decided to swap hinges on the high side, had a couple extra. Closed the hatch and it was waaay better, to within half a millimeter. Oh wait....I removed the weatherstrip in the corner to remove the hinge. I put the weatherstrip back on and right back where I was, 2 millimeters high. 🤣

Why didn't I do that to begin with? It's the &%$#@$%& aftermarket piece of crap weatherstrip they sell. Let me tell you something, I restored this entire car, sure I had struggles, but nothing compared to the struggle with these aftermarket hatch weatherstrips. Attempt #1: I carefully cleaned the weatherstrip of all residue, even scuffed up the area to be glued and cleaned again. Followed the instructions on that 3M super weatherstrip adhesive, did the corners first, taped it down. Next day, did the straight sections, taped it all down. Waited a couple days. All good right? I was doing something and happened to bump the corner, and it came off. It didn't stick! What? I gently lifted on the a section and it just basically fell off. That's where a 2 day nightmare started. Removing the 3M super weatherstrip adhesive, ☹️ It won't stick to this aftermarket weatherstrip at all, none, but have you ever tried to remove it from paint? Without damaging the paint? It took me 18 hours to get that black nightmare off. The hatch wouldn't close anyway. Every piece of aftermarket rubber I installed on this car with that 3M stuff didn't stick at all. So I cut sections of it up, and tried different adhesives. The best I found was goop. It's clear and it sticks way better. So, I ordered another hatch seal from a different place. Unfortunately it looked the same as the first, with spliced in "thicker bulkier" corner sections. That's the problem, I think, these spliced in sections. And that's where I am today. It really sucks. An old timer once told me, "it's made to sell, not to use".

I just went through the same hatch issue during my resto. Mine was also only an issue on the driver side. My body guy ended up bending inner edge of the hatch (the part that the seal goes on) to get the hatch to close flush. May not be the 'proper' way to do it, but it fits right and doesn't leak so I'm happy. I'm using an aftermarket seal.