Not sure how far you are going with your project, but the way I did both my cars, they were completely dis-assembled of every nut, bolt and washer so that everything could be cleaned down to bare metal and re-finished. If you want to accomplish that, it doesn't matter if you pull the doors off with their hinges or if you pull the doors off of the hinges still mounted on the jamb, then later pull the hinges off the jamb. Either way, the hinges are going to stand alone to get a complete cleaning, including on the hidden surfaces.
It may be easier to unbolt the door from the hinges to remove the door, then unbolt the hinges from the jamb. Each hinge has three bolts attaching it to the jamb. The middle bolt is in the middle so you will need 1/2", 6-point socket and long extension bar for the middle bolt.
I did not drill alignment holes since my hinges were so messed up to begin with, I needed to rebuild the hinges and start from scratch. But adjustment of the doors can be discussed in another thread.