When I put the Drivers side window up, its like the motor doesn't stop, it just makes this wierd machine gun sound when it is all the way up in the channel.. is it the motor or is there some sort of cut off sensor that is in there? I've never had the door panel off before..

 

Are you releasing the switch as the glass nears the top of its travel? I'd be more concerned if it made the noise when the 'one touch' down feature was used. That must be a 'learned' function of the GEM/SJB to monitor the amp draw of the motor to know when to quit trying to lower it through the bottom of the door.
The noise is likely the 'tape' that has square holes to mesh with a gear/sprocket to move the window. As the sprocket teeth keep turning, they will make a noise.
If the tape is going bad, the teeth will slip as the tension increases at the top of the glass travel. You may need a new 'tape'.
I have not searched for them to know availability. In some cases, the whole regulator assembly(EscapeTributeMariner) must be replaced. When those fail, the window many times drops to the bottom of its travel.
The other thing that can make the noise is the 'torque limiter', some of which are made using spring & ball pushed into 'detents', so when there is too much torque, the ***** will move out of the detents as the motor driven part continues to rotate, and they will make noise.
tom

add: Does the machine gun noise stop when you release the window switch?

 

The noise only starts when the window is all the way up, I'll have to check if it does it on the auto up too.. its operating as it should up and down, only in the full up, seated position is the funky noise starting.

 

Sounds like the description of a failing gear (last few teeth) on the window regulator.