What does everyone use to reattach there weatherstrip channel to the body? When I removed the channel, it had a thin adhesive strip between it and the body.

 

3m rubber cement for emblems and weatherstrip, black one.

 

Black 3M "strip calk" is sandwiched between the stainless steel roof rail channel and the roof.
Quite frankly, I don't use adhesive on the rail weather strip or the trunk seal.
The rubber profile holds/secures the roof rail in place. The trunk seal will hold water. On the rare occasion that I wash my 68, the non-glued trunk seal pulls out, I dry the channel, and reinstall.