yes the window first can work, might take 4 hands .... not clear about these 3 tracks, there is one channel that attaches to the bottom of the glass sash, then 1 short piece that should be welded to the inside of the door - there are arms on the regulator with wheels that slot into those, no "alignment" necessary or possible .... the track piece on the bottom of the glass needs to be slipped onto the regulator arm wheels when it's all inside the door
regulator pic, might help?
Bill