A better solution for the windows would be to remove them and replace the butyl tape. You have had 23 years of service out of them and new butyl should give that much more. It can be purchased at hardware stores ie. Lowes, Home Depot, Ace. After installing the windows run a small (1/8") bead of polyurethane caulk across the top of the frame and down the sides about 2".
For the roof there are two scools of thought. Some prefer to use Eternabond tape and cover over all seams, either over the old caulk, or remove the old and replace with Etermabond.
Others prefer Docor self leveling caulk, and just go over the old stuff.
In either case the area must be thoroughly cleaned to achieve the best bond. I would not recommend using silicone for any sealing.
There is a lot more work this way but the result will be worth the effort.
Harold & Linda
2009 CT coachworks siena 35V
W22 Workhorse 8.1L. Explorer Sport toad,