Help fix this leak. Lots of pictures

[Re-Pete]

So, here's the deal. We've got the shell back on our 92 Excella. We're stripping the old caulk off the back of seams etc. We're also finding some areas that have been leaking as evidenced by either missed or corrosion. Anyway, the plan is to replaced all of the caulk we're removing with Tremco's Trempro 635. A few of the areas we need to seal are gaps where the front window and the curved windows come together. I'm thinking of back filling them with Trempro and then front filling them with Parbond Aluminum for esthetics.

Besides the gaps at the windows we've also found a number of holes that were factory drilled or should I say misdrilled and because of access challenges never received a rivet and we're simply filled with caulk. And in one case where the antenna was moved, (possibly by a PO) to install the street side awning, they covered it with an emblem. I even found at least one unfilled rivet hole in the ceiling that was caulked. It did not appear to have leaked. For sure some did leak and some didn't. Out goal is to properly fix them all.
Any advice on the best way to repair / seal these is welcomed as well.