well the easiest way actually involves removing the fender.
Believe it or not the easiest way to swap the hinges is to never take the door off.
Take the fender off and unbolt the hinges from the door one at a time. Upper first then lower. As long as the door stays latched your adjustments would be minimal.
Since you have already done the swap, take your fender off and close the door.
The bolts that go into the pillar control your front to back and up and down adjustments. Do those first. Loosen all the hinge bolts going into the pillar. Get the gap between the front door and the rear door consistent top to bottom. Roughly 1/4 inch. You may have to pick up on the front of the door to do this. Once that is correct put the fender back on. The bolts going from the hinge into the door control your in and out adjustment. You want the fender to be an slight hair further out than the door. This will help reduce wind noise.
Good luck.