I really question the leak being at the clamshell joint. It is possible the water is wicking through the screws, but I really doubt it.
This is a cutaway of the clamshell overlap on a Northern Lite.

Although this is doable ; "... I'd consider completely removing all the clamshell trim (white metal and black rubber) and glassing (or epoxying) a seam across the two halves, forever sealing the unit.", I don't think this would solve your problem. I think you have a cabover side window caulk leak, possibly marker light or some other caulk failure.
I have a 1988 Bigfoot which is the same overall construction. I woke one rainy morning to find a pool of water under the matress. When I got home, I pulled the passenger side window, and discovered the window was not caulked properly. over twenty years before it leaked.

A couple of side photos of your TC would help us help you find the leak.
Wayne
EDIT: The butyl tape is what should be used on your windows, with no other caulking.

Tape squeezed out before trim with plastic knife

Excess being trimed
