Roof leaks in 1990 Custom Cruiser

I originally posted this under body issues but I think it is more appropriate under this section. Has anyone had this with their 80s boxy style GM wagon? One of my leaks comes down from the passenger side quarter window rear lower corner into the spare tire well on one side. The driver's side drips dead center top of the window from under the outboard side of the roof interior molding into the storage pocket. I just can't figure out if either of these are the windows or the rack. Any experience would be beneficial. It's been raining so I can't due a controlled leak test right now, my garage has another antique car in it. I knew about the spare tire well so I put truck bed liner in the bottom of it. The driver's side leak appeared last week when it was facing uphill. We stripped the droopy headliner down, I'm going to attempt to pull the cardboard out to check under it but the bottom of it is dry with no water residue. Hopefully I don't snap any roof interior trim hooks, does anyone have experience getting these out? Any pointers on the easiest way?