I have an older Kentrol top as well... I found that there was a very poor fit on the liftgate.
In order to get the gaps to appear somewhat close I had to add about 1/4" fiberglass possibly more to the left side to make the gaps appear even.
Other than than, just some filler to get rid of some of the waves. I still have not painted it entirely.
I had fiberglass doors, I removed the window frame rails added steel, I made sure that they matched the top when installing.
Only recently I removed the glass top, I have a soft top now. Keeping the glass top just in case I want to switch back. Before ever putting it back on I will make sure the paint is complete. I did not use or try to use the rear posts however I do not see any reason why you could not.
I used the gaskets for hole locations, drilled the top. Since my body was fiberglass I also had to drill all new holes in the body. I would work from the door frames, if you can't get that to match you may have to do some glass work there as well. I am glad not to be working with fiberglass, not fun, and very messy
-Ed