Can anyone tell me if there is a drain tube for the cowl on a TJ (like on the YJ's)?
If so, then your problem may very well be that. Under the hood, near the center of the firewall is a tube which comes from the air cowl. It is fairly wide, but tapers to a narrow slit at the bottom. It will collect bugs, pine needles, grime, and whatever else the road or trail throws your way. Eventually they become clogged then water from the cowl dumps inside the Jeep insted of out the drain tube.
I don't know if the TJ's have them, but it is a common problem with YJs. Maybe someone here will tell us if you have one, but it is easy enough to check and if you do, you will recognize it when you see it. It will probably be full of real nasty stuff. Pinch spring clip, remove tube, empty tube, replace tube. no more leak.
Another thing to consider is I always leave my floor plugs (and carpet) out through the warmer months. It beats getting into a pool.