I have a TJ wagon. There is water (when it rains) coming in through the roof at the rear somewhere. I have sealed the gap between the window surrounds and the roof in case it was that but its still coming in. The tail gate rubber is good - no sign of leaks there. Its coming down inside just in front of the tail gate from the area of the rear most window on both sides. I'm at a loss and would be grateful for any pointers. I cant see any related posts but I cant believe this is unique...

Is the side windows, is a common issue

You need to remove your interior trim, remove the windows (8mm nuts hold them on from inside) and then use some sort of NON HARDENING mutal mastic to re seal them after having removed the old seals

agree with mal, ive had this issue on 2 of my old 2nd gens and the current tf i have, takes me about 40mins to do mine and i o both sides at the same time