Popout glass replacement was tough, but I learn some things which may make it easier for you.
1. When removing the glass, try not to tweak the frame too much. Use a screwdriver to pry open the seam. Then pull really hard to bend the frame open to seperate the frame from the glass. Don't use metal tools or you'll damage the alumimum. You have to bend the frame to get it off, just avoid uneven bending that will require a big hammer to fix when re-installing. Heating the seal with a heat gun might help soften the rubber for easier release (I haven't tried this).
2. After powdercoating (good call) and tinting (if wanted), wrap the new seal around the window with the seam at the hinge. Wipe a little watered down liquid dish soap on the seal to help it seat in the frame.
3. Start at the back toward the popout latch and work your way back to the hinge. Push the glass into the frame all the way while keeping the seal even on each side of the glass. I used a rubber mallet and a wooden block to hammer the frame onto the glass until I heard it seat. Work your way around making sure it's fully seated as you go (otherwise, you may get a big gap at the frame seam because it's not seated along the way).
4. Insert the frame-to-body seal through the frame opening and work it around the frame. Lube up the seal with ArmorAll and feed it into the frame through the opening. Push it until it wrinkles, then pull the fed end it until it's stretched flat. Over and over again until it's all in. Or, you can use a small screwdriver to tuck one side of the seal flange into the frame without sliding the seal around the frame.
5. To attach the hinge you may need to use a padded bar clamp like I did to squeeze the top and bottom of the frame together. With too big a gap in the frame ends, the hinge won't fit. A bar clamp worked great.
Here's how it looks temporarily installed
Powdercoated popout latch
Hard work, but worth it now that it's done.
The method you described sounds great for the wing windows -- trace frame on plywood and scroll cut; attached cut plywood to backing board to support glass; lube seal with soapy water; load into wood fixture; pound flat edge of glass to seat seal/glass into frame using rubber mallet and/or board/hammer. That's how I plan on doing it for the wings (next week).
Later,
Bill