For those out of warranty and like to fix your own things, here is a quick guide for that clicking noise.
Chances are it is only the motor that is bad if it is clicking or thumping.
Not very hard to fix really. I think most of these cases are the motor gears stripping and not the doors themselves.
If you know how to take the center stack bezel around the radio off you are halfway there. Don't forget about the screw over the 115V out let. Take the bezel off then the two side 12V acc. plugs. Remove the ring bezel around the cup holder if equipped.
The culprit is the lower center motor, unplug remove two screws and remove.
If the gears are stripped you can position the big gear 180 out from the smaller gear. The door only travels about 120 degrees so won't hit the stripped part.
Reassemble and you should be good to go. 1 to 2 hours of your time. If you want to get a new motor it is about $40 from Chrysler.
Hopefully this is the extent of your problem.