Are you trying to be able to drop the tailgate, but still leave the window up?
During my body swap, my swapped in body didn't have the window track in the tailgate. I'm not thinking of putting it all back in, it's mostly offroad only anyway and the window is held up by 2 pieces of wood. I'm thinking of cutting out a window in lightweight plexiglass, somehow held up with latches or pins through the tailgate door, or something like that, so that I can some how push the window down by hand from the outside, and then drop the tailgate. The glass window is too heavy and awkward and slips out your fingers to do this and be able to pull it back up from the outside.
For you I'm thinking once the tailgate is dropped, you could slide the window back up and have some other latches holding that window up if you wanted to have it up like that.