DJ,
Every thing you've been told is good advice and I can't add to it so far as the hinges are concerned, but I read a tip on the car side that may help you reassemble it. Before you pull the doors drill a 1/8" hole through each hinge plate because 1/8" is just slightly smaller than the diameter of a 16p nail. When you're ready for reassembly drive a nail through the hole in the plate and into the hole you drilled along the hinge line and voila!, instant alignment once the bolts are started.
Don't drive the nails until you seat them or you'll pay the devil to get them out. The hole can easily be filled with Bondo but the holes will be so small they'll hide themselves and don't need filling, especially if there's a dab of paint on them.
Have fun.
-Randy