What do you all use for sealing under the metal strips that mount to the A-pillars and targa sails, that hold the weatherstripping? The original stuff seems like sticky black rubber.

Either thin strips of butyl or 3M Weatherstrip Adhesive.

Check adjustment of seals against glass before applying sealer.

Sounds desirable, but how is that possible? The aluminum tracks have to be mounted before the rubber weatherstripping is installed. Any adjustments would require pulling the rubber out and removing the aluminum. Am I missing something?

I think that is the point of a permanently flexible sealant. I rough fit mine without sealant just to make sure there was nothing major wrong, then pulled it apart and reinstalled with the sealant. The sealant stays gooey so you can adjust the trim at any time as needed.

Butyl. OE plus it'll allow a bit of adjustment if you find its necessary.

FYI, 3M the same except not OE. It cures to a very stretchy soft rubber that remains tacky. Not quite as tacky as butyl, but has very similar properties. I don't think it is any better than butyl, but a good substitute.