I know this thread is a couple months old but I too had this issue. The factory foam gasket is a POS. Mine was leaking on my Gen III truck so I actually went out and got a new housing because it was raining and I just paid $600 to have carpets replaced because of leaks that were a combo of an improper sunroof seal and the F'n 3rd brake light and I didn't want anymore water in the truck. The dealer water tested the truck after they installed the carpet and said all was well. I think they had a 4 yr old **** on the roof and when nothing came in said it was fixed. I ended up fixing the sunroof seal by readjusting the glass after going to wash it right after the carpets were replaced and saw water running down my back window but I did not realize the 3rd brake light was still leaking, thought it was just the drains for the sunroof getting overwhelmed because the sunroof was letting in too much water. Apparently the F'n dealer could not figure this the F out and told me not to park my truck on an angle anymore because it was overwhelming my sunroof drains, that's why it leaked. Yeah, right!! Anyway, I put a brand new housing in and that Fkr leaked too because of the stupid seal Chrysler puts on there. I had taken the old housing out and as an experiment replaced the factory seal, which was split, with a Rubber Foam Weather seal I picked up at Home Depot. The size of the seal is 3/8" x 3/16" x 10'. It cost like $3.

When I noticed the new one leaking after it rained all day I took the old one that I had put the above seal on and it rained like a **** that night. No leaks. Here is a pick of the stuff I used. To put it on I scrapped off the factory seal and then used GooGone to clean off the adhesive residue. The new seal is self adhesive like the factory one but it actually seems to keep water out. Why would you want that?

Weatherseal Tape
Attachment 13876