Thanks! Where is the starting point though? Do I need to loosen both and set my window level with the fixed small window and then tighten both. Also, my door is open so it's at the lowered level, do I need to remove the door connector with the switch depressed to make it set at the door closed position when setting these?

There is no official "starting" point.
It's literally trial and error.
Set both in the middle.
Raise the window.
Open the door.
Press the sensor/switch, is it too high? The lower one or both.
Too low? Raise one or both.
Rinse and repeat.

Also...
http://www.ft86club.com/forums/showp...73&postcount=2

Something is messed up. I pulled the plug out of the window controls while having the switch depressed so I can set it at closed height. I figured it was easier this way so I could line it up with the fixed window.

Now my window is stuck wide open and the control does nothing though I can hear the motor working (it will not raise). Is there a memory module I can reset?

Edit: Found a video for resetting this.

Done and everything looks close enough for me. The part I didn't get about these adjustments were that #1 and #2 were stoppers that make the window stop. I thought they were attached to the glass which is why I was confused about setting a starting point or whatever.

Pictured below is the window from my first post that was set way too high. It is now just a hair over the fixed small window which I think is ok to give it a snug fit when closed. On the drivers side which was not nearly as bad, the bolt is pretty much off the charts so I am guessing they adjusted something else that threw this off? I am going to tell them to not touch it, the last thing I want is them in there fiddling and breaking something else.

Thanks again, @Joon525

No problem.
Sorry for the short answers but I had limited time to get my own work done. Glad to see you're on your way to getting things back to where they should be.
Good luck with the body shop.