You can remove one hinge at a time. If the fender is off I believe you can remove one at a time while the door is closed. This would keep it all lined up nicely. Here is an old tech thread on the pins. - DOOR HINGE Pin Replacement 101 | Maverick/Comet Forums
Thank you for posting this question! I was literally wondering the same thing! A while ago I had a bushing go out on my driver's side door, and until now I was unsure about how to go about fixing it!