Like someone else said, the large door glass must go in before the vent glass. Ideally, it would be nice to have the felts removed as well, but since they're already installed, you may be able to work around them.
Feed the front of the glass through that cutout in the rear of the door, being careful not to scratch the paint with the metal frame on the bottom of the glass. It may be helpful to remove the stops from the window glass, but this is optional, and you can pretty easily work around it.
Once you get the door glass in, then install your vent window and then install the window track at the rear of the door. After all that, install the regulator.