Awhile back I bought another targa top from Jamie (jrust). At that time I went through the top and replaced all of the seals and painted the top with a flat black. As I have been storing the top in the trunk on rides I recently notice the top is getting scratched just above the rear rubber hold down on the drivers side. I also notice that the trunk is not closing completely on that side.
The question is what do I look for and how do I fix it? It appears the hold downs are in the correct location and the trunk lid closes correctly without the top inside.
I'll post some pictures later today.

I do know first had if the top is not centered side to side just right you get nice little paint scuffs on the top.

In addition to centering the top in the clips ......

Check if the mount for the rear hold-down is bent or somehow out of alignment, &/or if the mount & rubber bit is/are installed properly. There is a bit of play & adjustment in them in most cases. Make sure the rubber hold-down hasn't cracked to allow the top to bounce. If not any of these, then ......

Also see if the rear lid is lifting at the front left corner - setting it out of kilter towards the rear - if so, then your hinge plate or roller/etc. up there has failed or is out of alignment. Likewise, check if the deck lid is somehow warped, bent, dented - which I'm assuming it isn't since you'd see that easily from the outside & think that you'd mention it here, but the inner brace(s) could be and be less noticeable. Also look to see if the top has an odd warp, but I doubt that cuz you'd probably notice it in difficulty securing the top to the cabin.

If none of the above & if the car was in an accident or rust damage - either/both such that the rear end had some body work done on it & not fit up correctly &/or not Cellette Benched (or not done properly), then the uni-body could be out of whack.

If one of the front latches is damaged it may function to secure the roof to the car, but not fold properly for storage (actually go too far in the open direction). It can catch in the plastic cup and hold the roof tight to the trunk lid. I have one like this and find if I am very aware when putting the roof in the trunk all is well.

You might also have to adjust the trunk lid latching pin down a little letting it latch a little higher to latch....Remove it from the trunk lid (2- 10mm bolts) and loosen the big nut (17mm?) and adjust pin down a little....

The rubber bumpers in the corners of the rear lid are adjustable too. Unscrew them slightly to raise that corner only.