I see you cut the doors now...
was going to suggest that you had a look to see if it wasn't that after you'd finished cutting the roof that you weren't a few mm out, (which would account for the gap at the top of the door).
looking at the pics the door looks like it hangs a little low in the pictures, (with the lines on the fenders and the door). and if you'd got a little extra in the pillars then that'd account for the roof being too high, and the gap that you had to fill with weld and the gap at the top of the door.
just thinking that you might want to measure the wind screen, if you've added a few mm to the height of the roof then stock glass isn't going to fit any more.
(Though I think it'd have looked pretty bad ass with the roof left off and a flat panel wind screen/shield), kind of like an old willeys jeep on steroids).
(you'd have had to leave the back off then as well, but at least you wouldn't have to repair the fibreglas in that then either!