Can you start all of the bolts easily without forcing them? If not, I 'd recommending adjusting the brackets until you can. Also as you likely know, there's significant body flex in these cars and the top is actually under a good bit of stress when this occurs. It's treated as a structual member which is asking a lot from them, especially the clear tops. Adding an X frame from a convertible, or better yet an aftermarket one, helps significantly. Installing a harness bar or a roll bar is a big help too.
I bought and installed a painted top a couple of years ago and the clear top has resided in a closet ever since. I don't miss it a bit.
