I've had a bad water leak problem on my hardtop TJ since I bought it, I seem to have fixed it so hope this may help others.
Both the rear and drivers footwell would flood with water when it rained, I changed the hardtop muckets, I resealed the hardtop to the tub, I sealed the cold air intake under the front cowl, I checked everything and it still leaked in.
It turned out the rain water was running off the roof down the channel by the rear window seal then seeping in we're the rear window meets the tailgate and tub, it then flowed round the rear wheel arch and down into the rear footwell then it filtered under the drivers seat through to the drivers footwell.
I've now fitted an extra rubber strip seal to the bottom of the rear glass with some silicon sealant for good measure.
So far she stayed dry.