Do the quarter glasses seal in with silicon like the front windshield, or is it sealed with window tape? Or does it make a difference?

You can use either. Old school is window tape most guys would recommend window eld or something similar. Funny enough toyota still seels the original window tape if your trying to keep it owm. Lol

I used the tape, napa brand butyl rubber. Works great I don't have any leaks and its super easy to set and work with. I wouldn't use it on the front windshield lol but I make the argument that its quite suitable for the quarter glass. Cheaper and a lot less messy too. Just my opinion.

use the windshield adhesive it will last longer then the window tape

I don't know what the factory spec is but the usual adhesive is a urethane sealant, not silicone seal. Butyl tape is not a high strength adhesive, but there are newer tapes (like 3M's "VLB" that did not exist in 1985. VLB looks like black double-stick tape but when used properly, it holds big glass windows into skyscrapers without any other help.

Well, I'm glad someone asked.
This has been very informative for me .
Off to order some tape.
Thanks

Thanks for the help guys! I found exactly the tape I need....3M auto glass ribbon sealer.

oh yeah and in the factory service manual it tells you how to put on the window tape. If i can find it tomorrow i will take a pic for you it shows you how to end the seams so that water wont be able to get in easy.