Buy some shin-etsu grease and use them on all the rubber seals.

Adjust the striker plates on the windshield.

Put clear rubber tubing on the latch hooks.

That's all I got before removing everything and starting over again.

 

I tried the Shin-etsu grease, and I put something on the latch hooks, but the side as shown on the previous pictures still don't align. The driver side is still off.

 

Just in time. Just got to get it to align properly.

 

As said above, get the specific hardtop catchers. Easy install and works. This will help with squeaks and wind noise.

Take the panels off the inside of the hardtop. loosen the bolts to the bracket. Install hardtop and adjust the fitment. Tighten the bolts and replace panels. This is my vague memory of when I had to adjust the hardtop on my ap1. It was many years ago so I might be forgetting a detail or two.