I would try swapping the hinges from the old seat onto the new one and see if that helps. I'd also try leaving the bolts loose so they can be moved. Same with the seat latch.
I did an experiment with my CB500K seats and a bare frame. I had 2 seat pans, both OE, both with no foam on, just bare metal and rubbers. It's very easy to see where the rubbers land on the frame when the frames bare and the pans are too. Both pans didn't fit. Both had rubbers landing not aligned with the frame, the shaped ones at the front didn't land so the shape fitted the tube. Both had the seat lock poorly engaged, sometimes so badly it wouldn't unlock and I had to remove the nuts holding the latch to the pan before I could get them to disengage. Don't think the fitting the hinges onto the bolt holes means it lines up, it won't unless you're lucky. You can't see how misaligned it is due to the cover and the foam hiding the fact. It took me at least an hour and trying 3 different hinge bars before I was happy, then I found out the rear rubber doesn't touch the rear frame brace, it's suspended in the air, it needs to be about 3mm thicker to rest on the frame brace, both pans showed the same gap, it's why the pan snaps in the middle where the seat strap fits when you regularly carry a pillion like I did. One pan was broken in that area the other showed signs of breaking.
I mention this because it shows they probably never fitted perfectly from the factory, even though you'd think they would.
