[Model51]

I believe the original method of installation relied on the window channel material to seal the back window opening. I don't have a good enough original to determine if there was rubber material attached to the window channel or if they just relied on the fabric of the window channel material.
To be safe I'd run a small bead of black RTV on the inside lip of the back of the window opening, then press in the window glass with the window channel and then lock it down with the garnish molding strip and screws. You can wipe off any extra RTV from the outside of the glass.
It's mostly up to what you think is best and there's really no wrong way to go, but a small bead of RTV might be best.