I just FIXED this problem on my 2002 TJ hardtop. My problem was 2-fold (I found out later).
1st issue - Water coming in the back and soaking the rear carpet in the cargo area.
I replaced the rear-glass weather srtip (dealer only part - $114 - DIDN'T fix it).
I then noticed the 2nd issue - water pooling in the pass-side rear floor AND the front pass floor.
I replaced the pass-side door seal (full steel doors) - RESOLVED MOST of the leaking to the fron floor, no change on the pass-side rear floor.
After talking to a 4x4 shop (and reading here) I went to a canopy shop and spent $10 on a 25 ft roll of foam tape used to seal canopies to truck beds. My buddy has a hardtop lift system he fabricated with a Harbor Freight 3000lb winch ($50) and some ropes. We popped off my hardtop and resealed the whole thing, following the factory path, after cleaning off the old stuff that was about 1 millimeter thick. We replaced it with about 5-6 millimeter foam tape and were re-mounting it when I looked at the doors, just for giggles.
It turns out that the "gap" between the door and the windshield WASN'T STRAIGHT on the pass-side! I checked the driver's side and it was perfect from the bottom to the top. Just run your finger from the bottom of the widshield (between the windshield and the door) to the top. It should be almost perfectly "even".
My pass-side went from approx. 1/4 in at the bottom (like it should be) to 1/16th at the top, meaning that the door was bent out at the top thus not sealing as well as it should and still letting water into the rig (though slower with the new seal). My buddy and I blocked the door open and squeezed the top of the door by hand slowly and got it back in alignment almost perfectly.
After re-attaching the top (slide it forward until it's a 'smooth fit' in the rear, clamp down the front, then "snug" the 6 bolts down), it hasn't leaked a drop in a week worth of rain. I just pulled out the towels and replace all my Sahara carpet this afternoon.
One last thing... when tightening the bolts down, don't crank 'em down and white-knuckle them, just get them "good 'n' tight". Too tight and you'll squish and rip the new pad you put in and have to do it all over again. I plan to next winter after pulling the hardtop off and running the soft top through the spring and summer.
WHEW! Hope that helps.