ya I have noticed the shape of mine going down hill with just removing it for every summer and putting it back on for the winter 
Replace the seals under the top with the foam stuff you use on truck bed campers. It seems to work well as long as you don't slide the top around too much. You might want to use stick on weatherstripping on the top side of the doors and the windshield frame where the door closes. The doors will still slap a little under heavy winds.
When putting the top on make sure you have weight on the front to pull it down snug. Either have someone sit up there or else use ratchet straps You can connect two straps and throw it over the top. It will give you enough pressure to keep the top down. The other problem with the fops is that they aren't perfectly square. You might need to pull and push the sides from the back corner to get them to line up properly. It's always a PITA to get the doors line up properly. Better to pull and push the top then to readjust the doors every time you take the top off. Once you have the doors setup and the windshield angle set, it's best not to move them because you'll never get it all lined back up again. If you have a YJ top make sure you have the rubber bushing that fit between the windshield frame and the top. I'm not sure if a CJ top have these or not.
If you don't want to pull the top off you can always remove the doors and the rear glass. I just end up driving with the doors off and the glass on since I don't usually leave the Jeep with no doors on for long.
