I have not worked with the later headliners so I can offer no installation comments regarding it. However, the headliner can be cleaned and re-colored using spray vinyl dye. I have had very good luck with products from SEM. Your local paint supplier may have it. Eastwood and TCP Global (online) both sold SEM the last time I needed some.
You are correct, fit the glass to the body opening first. Tape it in place making sure that if you fit a continuous length seal (a opposed to close loop molded) that you butt the ends against each other firmly. (Cut the seal long and push then ends together. The seal will shrink over time).
Rest the glass in the bottom of the rubber seal, lean it forward and use a plastic spatula or plastic putty knife to lever the rubber up over the seal as you press the glass into/against the body opening. Generally this does not require any lube but K-Y Jelly works well if you need to get the rubber to slide over the glass.
Buy the lock-strip tool. You can make your own if you don't have the budget to buy the tool. However, do not try to put the lock strip in with a screwdriver or similar. While it can be done that way, you risk hurting yourself or the car if you use a screwdriver. Run the lock-strip all the way around the seal and when you get back to the starting point, cut the lock-strip long (like the bulk rubber seal if used). Put the finishing clip on first, then finish pushing the locks-strip in place. Slide the finisher clip over the lock-strip butt joint. As with fitting the rubber to the glass, K-Y Jelly works well for easing the lock-strip in place.
It should go without saying that the bodywork needs to be rust free and in good shape if you expect this to seal. Use new rubber, not an old hard seal. If you doubt the ability of the rubber to seal against the bodywork or glass, you can use the black sealing goo for glass but I don't use that anymore. At the parts store look for Permatex flowable windshield sealant. It is a very soft, thin, free-flowing RTV sealant. It can wick into tiny cracks to seal voids. It remains pliable, is easier to remove than regular RTV, and is much cleaner/easier to work with than the black goo. If you are convinced (in advance) that you need sealant, you can apply it under the edge of the seal to the bodywork and between the glass and rubber before you fit the lock-strip. When the lock-strip is fitted the excess Permatex will squirt out and you can wipe it away with paper towels.