When the window gets within about an inch of being fully closed, there is a THUNK coming from down within the door. The motion of with window remains smooth and closes properly. Any ideas as to what is happening inside the door?

 

Something is skipping or off track. I would pull the door cover and operate the window up and down. Look into the door regulator area and see whats going on.

 

definitely pull the door card and look. may be a window clip or its bolt inside it is loose, and just requires slight tightening (do NOT over tighten or you will break he plastic)

 

The noise is GREATLY reduced. That leads me to believe that it may be temperature related to an extent. We do have summer days where it can be 122F here in the desert.

 

Yep my guess is that its the cord that cuts across the regulator or the seal

 

You can check to see if the bolts that hold the glass in (they go through the window) might have come loose without taking the door apart. It's easy to check before you go into the much harder take apart since you really can't see inside the door and how it's working without taking the glass out and removing the entire regulator. (it comes out as a unit)

to check the bolt tightness:

take the metal trim on the outside of the window off by pulling it up, should come off pretty easy

Look down inside the door on the outside of the window. you'll see two large "gears", those are actually the nuts that the window bolts go into. you can reach in with a screwdriver and turn those "nuts" to loosen or tighten the window. This is how you adjust the glass after you install it to make sure it's straight in the opening.

But if one of those is loose the window will move around while the regulator is moving it. The hole in the glass is about 2X the size of the bolt so if one of them comes loose you can surely get a clunk as things shift.


(there are videos on youtube on how to adjust the glass, I'll not go into that detail)

 

I remembered something that I didn’t mention before. There is a white “skid mark” (for the want of a better term) on the inside of the glass about 2” from the front. It rubs off pretty easily. Could this be what is dragging?

 

that "skidmark" is a guide in the door that keeps the window glass in place. It run against the glass for the whole length of the travel.

I can't remember how it's attached though, but I doubt that is your issue.

 

OK, just thought I would mention it as you never know what detail might be significant; particularly as I’ve never seen the inside of these doors.