My leak was from the super top retainer channel at the top of the windshield.
The bar is extruded aluminum, but the finish off the ends with plastic caps to get the curve in there...they are rivited to the aluminum. One of the rivits broke causing a slight gap between the plastic cap and the aluminum.
I didn't fix that really...I just adjusted the clamps for the bar so it would pull down tighter and straighter on the top of the windshield....closed the gap enough for now.
Actually buying a new bar today...less than $30 and I have a $50 gift certificate to 4WD.
On the TJ, you may want to run a bead of sealant around the vent cap under the cowl...looking at the front of the Jeep, it is on the way left side of the cowl area. If that seal is okay, nothing short of a flood coming over the hood would let water up high enough to get in there...unless the drain hole is plugged really bad.