stevejumpr,
For my last 12 hinges (last two trucks), I used a hydraulic press to remove the pins. After the pins were removed, if the various holes had to increased for bushings or oversized pins, I used a drill press.
You might be interested in this technical article:
http://www.classictruckshop.com/door_hinge.asp As far as rehanging the side-doors properly: practice and patience and a lot of time are required. Maybe someone else will have more helpful advice on rehanging the doors.
Good luck,
Tim