The problem is very likely to be the seal for the Center High Mount Stop Lamp (CHMSL) on the rear of the cab. The seals on the CHMSL are a known issue that will allow water to saturate the headliner and leak from the lowest point. That was probably the issue all along, although having clean sunroof drains are good anyway. There are a few posts and videos showing the issue with the CHMSL. Fortunately the size of the seal is pretty typical for window and door weather stripping available from most hardware stores. Clean off the old weather seal adhesive and apply some closed cell self-adhesive weather stripping comparable in size and your leak will likely be fixed.

-Rod

 

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