Debris was not a big issue here. The nearest tall tree was 50 yards away and was an evergreen. This area is mostly evergreens and palms, so few leaves to blow onto the roof.
It rains under 20" per year here, but does rain hard several times a year. In Seattle I might have done this differently, but here is what I did here -
The valleys were hot mopped up 3 feet on each side; then we built a cricket that sloped from +12" at the front of the valley to 0" at the back; then covered all with a cap sheet up 2 feet on each side; hot sealed all the joints; then shingled over that. Even though it is a 10/12 roof we treated these valley areas as if they were under 3/12 (which the cricket actually was). The water drains to a large 6"x 6" gutter at the center section and then under the deck and patio stone directly into a 20" deep Bio-Aquifer reservoir under the driveway. The drain that is in the middle at the bottom of the screen drains only the patio which slopes to its own center floor drain. Though we added about 700 sq ft of new roof, and about 1000 sq ft of other hardscape, all the run off water is contained on the lot.
Sorry I do not have a photo that shows this better.
Your situation sounds complicated. Water is the main enemy of all housing. Figure what you want to do and then double it just to be sure. Velux skylights are very good. Never skimp on roofing materials if you can. As the old TV commercial says - "you can pay me now or you can pay me more later" !