hi utey,
just going through the same dramas with painting etc:
just gave my sedan a complete bare metal respray in and out, in solid and COB. after painting i had to remove doors to install full rubber kit then put doors back on. this is a nightmare, as the doors sat well before the rubbers went in but after hmmmmm!
im with Ed on leaving the windows and regulators out until completly happy with alignment the doors are heavy enough as it is.
if like me you cant wait till someone drops around to help hold the doors up while you align everything a little trick i found worked quite well was to use two trolley jacks one under the leading edge and one under the trailing edge of the door. this way you can lift the back / or front without everything else moving. just take your time. and walk away when frustrated
hope it helped a bit
dean