John I have added a hard top to quite a few Jeeps. I have found adding two strips of the sticky soft rubber tape to the sealing area of the windshield frame (where the top will sit) and then adding one strip to the side rails of the Jeep, keeps any unwanted rain or dust out of the Jeep.
Then I set the top in place and SHUT the doors making sure the top isin correcty for the doors to work..

THEN I always put a friend up on the top. I have him SIT on the top in the middle of the windshield. His weight insures a leak proof seal while I install the screws to hold the top in place to the frame of the windshield.

THEN I check the door fit again. Next I install the hold down bolts to the side rails. I ALWAYS use the nuts with NYLON in them so they will not shake loose. Nothing is worse than having the top come off at sixty miles an hour on a busy hiway.

The windshield is adjustable forward and backward by way of the roll-over frame. The adjustment is controlled with the bolts on the TOP of the frame. I have found several Jeeps that needed the windshield moved one way or another to make the new top fit correctly to the doors.

Hopefully this will help in your install.
Big Jim <img src="/forums/images/graemlins/pfft.gif" alt="" />