Very nice! Dicor self leveling caulk is the cat's meow for finishing those screw heads and edges of roof "holes". Another product I have used successfully for many years is "NP-1" caulk. It will stick to just about anything. (Wrote an article about its many uses published in PA some time back)
Living in HAIL country, I have replaced the sewage vent pipe covers with metal instead of plastic. I also build 2" X 6" boxes covered with 3/4" plywood to fit over all of the "skylights/vents" to protect them from the "hard rain". Sure has saved many replacement costs over the years. Just have to remember to remove them from the roof before going down the road!
A metal vent cover replaced the plastic "skylight" on my pickup camper which has saved it over the years.
Nice job. It will be well worth it for many years to come.