Yep, pretty much all of us here don't like MoPar for the body finishing but rather for the indestructible drive train and bullet proof engines!
I have spent a lot of time aligning doors on different cars for me and other people and I can pass on the following info:
Looking at the roll - pitch - yaw drawing in the link for reference your adjustment will consist of the following motions (with the exception of yaw):
http://developer.valvesoftware.com/w/images/7/7e/Roll_pitch_yaw.gif
In addition to the rotation about the X and Y axis, you will have lateral movement there as well.
You may need some serious implements of destruction to make your door fit well. Rubber mallets, BFH, pieces of heater hose, floor jack, wood and maybe pry bars. I use the quarter panel as my point of reference and adjust the door, fenders and hood to that. The bottom gap along the sil plate is usually huge on the MoPars so don't go crazy trying to get that tight. Another trick is you can spread the error over all the gaps rather than getting three gaps perfect and having a huge gap at the fender or something. Also don't over look twisting the door to make it fit.
Rubber mallet and BFH - Help move stuck hinges or ????
Pieces of heater hose - Strategically placed between a section of door and body and used as a tool to deform the metal by forcefully closing the door on the piece of hose.
Floor jack - used to jack up the car (a little) by the open door to do more deformation, or with the hinges tightened just to the point of slippage under a bit of force, to move the door in a controlled fashion.
Wood - Protect bottom of the door from the jack; other adjustments.
And don't forget the window fit to the roof rail and getting the striker correct. You don't want the striker to put the door into a bind as it latches.
It's a lot easier to show you but I hope this attempt at describing what I do is useful.