Okay so here's the driver side, I took a BUNCH of pics, so it should help with the install on the other doors.
So here we go, motor plug with the dark blue and brown wires:

Remember since this is the driver door we're adding the auto UP feature, so we cut the dark blue wire. If you were adding the auto DOWN feature, you would perform these steps to the BROWN wire.
Cut the dark blue wire and strip the ends:

Connect the HARNESS side of the dark blue wire to pin 2 of the module:

Connect pin 1 of the module to the dark blue wire going to the motor connector, no pic, but you will see it later.
Connect pin 4 for the module to the brown wire (If you were adding auto DOWN, you'd be doing this to the dark blue wire) of the motor, the brown wire is still connected to the motor, the pin 4 wire just taps into the wire:

Then you should have 3 of the 5 wires running to the module connected, Pin 1,2, and 4:

All that's left now is power and ground. This is the yellow wire that supplies the +12v to the power windows, and will supply the +12v to the module:

You have to tap into it just like we did with the brown wire above, and I chose to tap into it closer to the door instead of closer to the switch plug. This way there is les wire run to the module, and you don't have to worry about the plug reaching the window switch on the door panel. Here's the splice, before soldering:

Then connect pin 5 to ground, and connect everything up for a test run:

http://www.youtube.com/watch?v=CJIpzJ7pick
Once you know it all works as planned, wrap up all wires so they don't get caught up in the window, and find somewhere to mount the module. Here's a pic of mine, you can also see the grounding spot I used...the module is the blue box you can barely see on the slight left:

Now go ahead and put it all back together, you're done! I still have to pull the passenger side back out, but I'm out of zip ties to mount the modules so it'll wait a day or 2.