My aftermarket hardtops (I'm on my second one - first one was a Fleet Air, I think current one is too - dealer installed original one, insurance company bought second one after a black ice roll-over) leaked. Both of them. Water gets in with almost every rain. Spraying with a hose is plenty to cause leaking. I tried everything on the first hard top to fix the leaking. It just wasn't possible. Most of the leaks were and still are around the front doors. Sometimes the rear window leaks - both hard tops. I replaced seals and tried adjusting the position of everything adjustable. Both of these hardtops leaked from day one and the one I have now leaks to this day. The bottom line is I finally gave up and just live with it. I keep a couple of large pieces of towel handy so I can wipe off the water on door and seat when necessary. If I ever have to get another hardtop I'll do my research first and find out which hardtop the members of this forum recommend. Sounds like there are some available that don't have the leaking problems my junky hardtops had and have.
Also, I was blaming the hardtop for a lot of water on my floorboard on passenger side when I'd had my TJ a couple of years. I finally called the dealer since the warranty was in effect and convinced the service manager to find and fix the leak. Turns out it was the rubber boot that fit over the cowl drain causing most of the problem. It was full of crap, mostly pine needles and leaves. The fix was to take the rubber boot off and throw it away. That drain needs to be checked once in a while and kept clear. If it clogs up water fills the plenum under the cowl and ends up running into the ventilation system.
White '97 Sport 4L with Flip-top hard-top
Not-so-Fat BFG ATs
AFE cat-back exhaust with Magna-flow cat, all stainless
K&N cold-air intake with throttle body spacer