on my 98 f-150 flairside it did the same thing the water was coming in from under the break light. Pull it off and check you may need to seal it I used some clear silicone caulk to fix it
Ford had problems with the slider backglass sealing properly in those years. Yes it does need to come out and be resealed right. Should only take an hour if taken to a GOOD glass shop. Just don't reseal with silicone, that is only a quick fix,won't last.
Took my 2000 L in for the same problem after warranty and my service advisor only charged me a $50 deductible and Ford covered everything else. I had two other problems fixed at the same time too late Stan
mine did too. Took it to a glass shop to have it resealed and it ended up being the gromet dissapeared that the 3rd brake light wires run through. Weird since i never took it off and it didn't leak before. Did fix the leak and costs me $20 instead of $100+ to fix