So I can finally label this project as complete. All windows have up and down (or open and close if you look at the sunroof), my alarm closes the windows every time I lock the doors (but if I lock them with the door switch nothing happens), I can open all 4 windows with one channel on the alarm, and open the sun-roof with another channel. This was all done with 9 one touch modules (2 for each door and 1 for the "close" side of the sunroof), and a sh*t ton of relays (12 or 13). Point is these things really allow you to manipulate your windows however you want and are free\cheap at the junkyard.

Only thing I may have left out was to mount the boxes with wires facing down so they don't fill up with water. Ask me how I know...

Here's a video of the alarm working with the one touch modules. Your window switches would do the same thing whenever the car is on, tap "Up" on a switch, that window will roll all the way up, tap "Down" it'll roll all the way down. Want the window to stop? Tap the same direction you are going again.