did the previous owner of the hard top add their own weather stripping to the hard top? maybe theirs was leaking so they put some extra on to seal it up.
there's really not much alignment that you can do with a hard top. when i put mine back on i got the 6 bolts in finger tight, secured the windshield channel, shut the doors and then tightened the body bolts. maybe the back of the top is too close to the front and it's causing the door jamb to be slightly squished.
try loosening up the 6 body bolts, give a little pull from the back with the doors shut, and tighten them back up. see if that helps.