With a small amount of additional shaving, I believe I've come up with a side window glass pattern that works for a single panel of glass. currently I am using corrugated plastic that's very close to the stock glass thickness and bent it to the same curve as the glass. It's attached to the lift mechanism, and it moves up and down freely.
As shown in the image above, the small triangular opening needs to be filled with a black metal filler chanel that reaches down into the door to serve as a guide for the front edge of the glass as it drops down into the door. This channel should attach neatly to the inside of the window frame. So far, I've done nothing that's not reversable to stock.
The next step is to fabricate the same in plexiglass.