When I did it, I also built in the ability to play 8 screens at once, assuming that they are laid out the way I do them-- four on the left monitor, four on the right. In order to do this, I started using the joysticks. The left joystick takes you to the four windows on the left monitor, and the right joystick takes you to the four windows on the right one. I'm assuming 1600x1200 monitors, but that can be changed by editing a couple of numbers at the very top.
Other than that, everything should work exactly as it did before. If you don't have a second monitor and four more windows going, you can just ignore the right joystick. The index-finger buttons also still work for the lefthand monitor.
Consider this beta, but I've been using it for a couple of hours and it's been stable. The new script is at http://www.pattib.org/StarsSNGGamePad.ahk for now. I think I'll put up a webpage for it in a bit.