The problem you have is not unique. Try the following:
1. Make sure the winshield is square to the tub. There is some movement. If it's skewed to one side then one side will fit agianst the doors while the other will not.
2. Loosen all door hinge bolts, on the body and on the tub.
3. Make up about a 1/4" to 1/2" thick by 1' cardboard strip.
4. Tape the strip down on the bottom door sil of the tub.
5. Slowly close the door.
6. Watch the door frame as it should just slightly clear, or compress evenly, the strip.
7. When the door's closed (and it should close easily.... no slamming or jarring it closed) then look at the leading edge of the door. Is the gap between the door and the tub even and straight?
8. If not, the correct the allingment using this as you're first alingment point.
9. Once alinged then look at the windshield gap. If there is still a gap, traditionally there will be a slight gap at the top.
The hard doors on my CJ hang perfectly and can be shut against the tub extreemly easily. Make sure the door post is correctly aligned to hold the doors against the body of the tub.
If there is a gap, and it may NOT be able to be adjusted out, then use some sticky back foam you can get a the hardware store and put a strip along the windshield frame.