I didn't read you whole post, but on skylights...When I did my skylights, I had to call the manufacture about something. In talking with their tech dept and they said only to use "SB 140". As other sealants "might" react to the type of plastic used in skylights. The SB 140 works good as a sealant but a real pain to work with. Also I used 3/4 inch fender washers to dissipate stress.
Also be careful about any wires are located near the skylight, if you're making new screw holes. Don't get wires mixed up in screws.
If roof is that KO'd, why not just replace and be done with it?
