:laugh:
Okay, I'll try my best to answer all your questions...Bear with me..
Work can be done off the jeep, as long as the top is sitting Flat, not tweaked or torqued.
The opening should be reasonably clean. Some old sealant can remain as long as there are no gobs or chunks of old sealant that would prevent the glass from laying up flat in the opening. Clean the area with Acetone or Alcohol, clean and DRY is the goal here.
Dry-fit the glass to get the lay of the land, see where things line up and how much coverage you have. Don't forget your rubber block.
A light bead of sealant on the flange, 3/16" or so, will do on the opening flanges. Press glass in gently, there may be some "squishing out" ( Industry Term), which is okay.
Sealing up simply means that after the glass is set, go around the glass with a Popsicle stick (or Polycarbonate Dressing Tool, whichever is closest) and tool the sealant into the joint to ensure complete coverage between glass and Flange. You may need to add some more sealant here and there as you go. Tape the glass to the hardtop in a few spots to keep it from shifting.
This is important. There must be a gap all the way around the glass for the "T" leg of the weatherstrip to lock into, 1/8" or so, so don"t fill it all up with the sealant, just around the glass edge. I'd let it sit at least overnight or until there's no transfer to your fingers.
Excess sealant can be cleaned off the glass with a single edge razor blade after it cures.
Install the new trim, probably have to cut it to length, put the joint and End Caps at center, bottom.
When you look at the new trim pieces, you"ll understand about the gap.
That should do it.