OK, here is what my buddy suggests:
Cut a frame plate for inside and out with the frame having 3/4"~1" overhang into the window opening. have your glass cut loose, about 1/8" gap all round. Stitch weld the inner frame. When it comes time to mount, drop the glass in with spacers to keep the gap even. apply high temp silicon in 2~3" lengths around the window, let harden (apply shallow though-just enough to hold the window in place). Remove the spacers, apply more silicone around entire window gap. install outer frame (tapped with machine screws).
You want the final silicone application to be raised about 1/16" above the glass for a good seal on the outside.
Of course, you would need to install the inner frame and tap the outer frame along with the heater box where the frame is to be installed prior to painting. Then install the window after painting.
Hope this helps