i don't know much about the 95 accord, but i'm in the middle of reupholstering and painting my interior right now in my 96 civic ex. it seems like there has to be some way to remove those panels completely, you may be missing something plastic that can be removed to gain access to a screw or two.
as far as the touch-up paint, i'm using duplicolor to paint it so i'll be using smaller cans of duplicolor and a small paintbrush to repair any scratches.
hopefully someone will reply to your question about reuphostering the sunroof headliner, i was wondering about this myself.
btw, are you applying the new material on the door panels directly onto the plastic panel or are you padding it?