I bought my car with a home owner special top job. After hard rains I had 3-4" of water behind the front seats. I tried to patch small weatherstrip holes etc. even the car wash water squirted in from all angles.
I did a lot of reading and ultimately decided to have a trusted top shop take it off and redo it. I haven't had a single drop of water since. I even hit it with a pressure washer and not a drop.
Moral of the story is that I'd have a pro do it. And this is coming from an avid DIYer who has done 3 Jeep tops before