Ok, so we are talking about two different uses for the relays. I'm going to go ahead and install the wiring using the single relay mod as shown in Fleet72's little sketch up. I don't expect this to make the windows perform any better than the stock setup, but it will make for a clean and easy install. The other relay mod would be to install 2 relays per door, one for up and one for down. This would take the load of of the switches, reduce the voltage drop, extend the life of the switches, and hopefully speed up the windows by providing full voltage to the motors.
I'm going to get the doors installed with the one relay for the harness just to get started. Once they are in I plan on tearing the doors apart to clean the tracks, rollers, insides of the motors and switches. I also picked up some garage door spray lubricant to slick everything up. Once I'm this far, I want to try the relay mod to speed things up (2 per door). I found this diagram that looks like it should do the trick. Let me know what you guys think.
http://www.thestreetrodstore.com/Doc...icWindows1.pdf