FWIW - I'm right there with ya, so I'll be watching for advice/info myself.
I'm in the process of doing the same thing... except, I'm going from scratch with manual roll-up quarters (conversion with coupe parts) and doors (with an aftermarket power window kit for both).
So far, the doors are loaded up with glass and outer felts, and the new drip rail trim is installed - Installing "new" glass (from my '72 parts Mach 1) was just a matter of putting the glass back in, and lining up the bolts with their corresponding "clean spots" on the regulator bracket.
We spent yesterday cleaning the quarter window roll-up mechanisms and weather stripping channels (door rails). Studying both the Yellow Body Assembly and Interior Assembly Manuals, and seeing how it goes back together, my next step is to install the headliner, as the door rails over the doors/quarter windows seem to be right up against where the headliner material will be secured to them - easier to do the headliner with as little in the way as possible, as I understand it. After that, I'll be working on the quarter roll-ups, door rails, and weather stripping... and getting it all lined up (before installing the Autoloc window motors and power locks).
Any advice on lining up the windows and quarter windows to prevent leaks will be huge and greatly appreciated. Thanks in advance!