I have changed over the glass and window mechanism to a new door. The door rolls up fine, but will only roll down until it is about 3 " from flush and then it binds.It seems as though it may want to roll up farther than it should also...

Anyone have any advice?

I would check the rear piece that the back of the window slides in could be in upside down.

Do you mean the small bar that runs horizontal, that the mechansim tracks in? What do you mean by upside down, does 1 side have to face toward the front of the car or does it matter?

part #9 on page 6-32 of the Service Manual, called the rear guide.