They usually have expanded metal or bars so you don't hit your window when loading stuff and you can also secure cargo to it instead of the roof contacting the cargo (lumber, ladders, etc.)
Yes, supply line to the fuel rail is o-ring/spacer/o-ring. The regulator has a single o-ring where it attaches to the fuel rail (I think same size as injector o- rings) but o-ring/spacer/o-ring going out to the return.
All three places where the o-rings and spacers are used in the 4.0L are the same size. The difference is between RENIX and HO, HO are larger. For RENIX the original PN for the repair package was 83502745, same for the 2.5L engine, #25 below.
I have a bezel, looks like the yellow has faded, there's a chip in the lower right corner and looks like one of the tabs on the back has broken off (I assume there should be four). $5 shipped, pm if interested.
I think the inner shift boot is no longer available, but there is one that works https://www.quadratec.com/p/crown-automotive/interior-shift-boot-97-02-jeep-wrangler-tj