Hi, I have the Bestop soft top for my 95yj.(the tinted one) I haven't had any problems with it... you might want to check if its off centered... you might have too much on one side and not enough on the other... try taking the whole thing off and puttting it back on... Also, how cold is it out where you are... when the temp us below 60 degrees, it makes the fabric shrink.. or harder to strech and install.. in that cause, what I do is leave the "V" bar by the rear window the last thing to extend. Also, do you have the correct top for your jeep year?... It can also be defective. If its just the bottoms above the door.. you should be able to slide them to line up.. you can replace those as well if they are old and rusty, and they aren't too expensive. from what I've heard, Bestops are the "best top" for a jeep
Let me know if you do the TJ conversion. Sounds interesting.