There's two possible reasons the doors won't close. The first is the contacts in the motor. You're going to replace the motor, so that may solve that. It's been my experience that the biggest problem with the motor is the lower bearing gets dry and needs to be cleaned up and greased. They come apart pretty easy and whatever you do, don't bother sending it out to be "rebuilt". I won't get into it names and specifics, I'll just say that you don't want to use that service.
The other problem could be the relay under the dash. A replacement is $$$ and since it also fits a Charger, they get $$$. A Bosch/Tyco relay can be substituted with a little rewiring. That's on my winter punch list as the stock relay doesn't play well with my added headlight relay. When I do it, I'll write it up.