Seeing your pictures takes me back to when I was stripping my bus. Yours looks nearly identical to mine.
I'd definitely suggest that you remove the inner window trim rings and strip off the side wall fiberglass trim panels also. Once they're out you can check the body around the window cut outs for water damage from leaks around the windows. If water gets in between the inner and outer body panels it can ruin the corrugated "filler" between the panels and leave you with floppy walls. I had to repair about 5 feet of one side where water had seeped in at the wheelchair lift door over the years and separated the panels under the windows. The job was technically interesting but not much fun.
Six of my fourteen windows also had leaks between the window frame and body so I resealed all of them. A fairly easy job.
Roof leaks can come from the exterior trim pieces where the body sections come together. I used a Dicor RV roof sealant to seal all of them and so far no more leaks.
I like the new sky light window!