[68Timber]

It'd be good to get some input from a paint and body guy. Offhand I'd say wait until you get the truck back so you can trial fit them before you glue them into place. But you may also need to give the paint some time to harden before you put the top on for the first time.

Where did you get your seals? Be careful, there is some junk out there. I bought a new tailgate glass outer seal from LMC, it looked like it was as old as the truck in a year. There's a vendor here that sells better stuff but I don't recall who at the moment.