If it were me, I would start with getting the windshield in the correct position for the windows to align correctly when raised. Then I would attach the hard top to see how it fits.
I also have a surrey top on my car and had no problems when I disassembled and reassembled the car. And that included removing the windshield and hard top pieces. There is very little room for the rear window to be adjusted on the car. However, I am of the opinion that if you were to loosely assemble the rear window and hardtop onto the car and see how they fit, you might be able to make any small adjustments to get it to fit better once the windshield is in its proper place. But I would start with the windshield free of the hard top.
There are two bolts that hold the base of the windshield in place. I just worked on a TR6 that was missing one of the bolts on each side. The result was the window glass would not align with the windshield. Once both bolts were in place we were able to correct the windshield angle. We did this as a preparation to putting a hardtop on this car. I doubt that the hardtop would have fit had we not started with correcting the windshield angle.
Charley Fitch
