Yes, that's pretty much what I did.I drew a little diagram based on what you described. Does it look right to you? Thanks.
I think that's the nicest system I've seen. I tried to use a similar window seal from McMaster-Carr, but it was too bulky and bulbous, so I went the riveted route. If I'd known about the RW-59 window seal, I'd have tried it. I just checked to see if I could cut my existing panels back to the rivet holes and use the RW-59 seal, but it appears the crossbar in the window will prevent that.Here's another method to consider and it's what I used on my Taylorcraft.
USed a similar grmmet in CNC controller cabinets when they're pressurized with shop air to keep stray carbon fiber out the electronicsHere's another method to consider and it's what I used on my Taylorcraft.
You build the frames around your windows just the same as described above but when it comes to installing the windows you cut them about 1/8" smaller than the hole in the frame all the way around and install using a one-piece seal grommet. The material can be bought from Spaenaur and probably other sources as well.
It makes a very clean installation inside and out and is water tight with no issues. It does not require drilling holes through the plexiglass and does not require additional sealants so it's easy to remopve and replace if needed. Only downside is it's a little bit fiddly to install first time till you get the hang of it and the material comes in minimum 50' lengths but hey! Once all your airport buddies see how good it works they'll want to buy your left overs for their projects!
Fun Fact; I stole the idea from deHaviland, they use the same grommet/seal to install the passenger side windows on the DHC-3 Otter. I had a chance to work on the aircraft in the picture as well as the rest of their fleet back in the 90's when I was rebuilding the Taylorcraft.