Finished this job, I cut new windows with a jig saw ~3 mm's outside of the old windows, taped together as a guide. I then took the template old window with the new plexiglass to my router table, where I got a flush cut with the old window.
I then rerouted it with a 45 degree angle, after reading that Sika 295 UV (one of maybe 2 caulks rated for plexiglass) wanted a large bead (I think it was 3/8") to account for expansion and contraction. I figured that the 45 degree angle would buy me a larger bead, as the old gasket was <1/8" think, while maintaining the size and most of the strength. The sika 295 requires a primer, which I applied in two coats, because even after sanding it was tricky to get it to bind much to the plexiglass.
You can see the 45 degree and the thin primer running over the edge onto the paper still protecting the body of the plexiglass.
After that I used a massive amount of 295, wiping up the excess. It took me too long to realize I should have had the frames taped to protect them from the primer and caulk, so my first one was a lot uglier. Lastly, I used 1/8" butyl tape between the frames and the body, secured with same back side of the frame as is originally present.
If I was to do it again, I'd strongly consider cutting slightly bigger windows and doing a flush on body type design thats more popular these days. I say that because these frames still look ugly and have some corrosion on the aluminum since they are approaching 50 years old. Either way, my boat is much much more dry since I did it.
I'll try to find more photos, I know I took them, hopefully they are on my work computer.