Hey I know many of you have experienced this same issue with water leaking in around your doors with a soft tops, nearly every post I have read regarding this mentions water showing up on the door handles.
I bought my Jeep about two weeks ago used and was the first to take the top off. After doing so there were a few storms in my area and my carpets were soaked in the mornings with water visibly on the door handles. It had to be something I was doing or else being a 2009 -- the carpets would have started growing mushrooms
This is my third Jeep so I doubted it was due to the way I put the soft top back on.
I took the top down over and over again. Purchased weather stripping from lowes, and tried my hand at strategic duct tape. Nothing helped.
Fixed it tonight !!
I have the soft top with sunrider option as most everyone does, and after raising the sunrider part I left the plastic sieve or sleeve moved up so I can raise it quicker. I noticed this created a bulge in the top at the exact area it was leaking. After moving the sleeve back onto the area which "locks" the sunrider elbow. No Leaks...Ive thrown hoses, water bottles and a drive through car wash at it.. Dry.
I hope this helps some of you that struggle with this. It cant be the cause of every leak but I bet its a few.