We decided to use butyl tape as our bedding compound due to the fact that it has a 30+ year service life and we'd read a great post about it on Sundowner Sails Again that convinced us. For the port in the photo below, we just used butly from Napa Auto Parts (used for windshields), but it was a lot harder to work with. The link to the really good butyl mentioned on Sundowner's page is here. We used it for all the other ports and various rebedding projects and it worked waaaaay better!
On the exterior, we used Lifeseal to waterproof around the bolt holes and secure the outer ring of the port.
We secured the outer ring of the port light with a clamp so that we could get the bolts back in (sorry no photo). Remember to mark which bolt goes in which hole because ours apparently had specific spots. Our coach roof and headliner varied greatly in thickness and each bolt was trimmed accordingly which matters when you have a cap nut on the end. We realized this after the fact and had to figure out, by trial and error, where each one went!
The finished product all shiny and watertight!