The easiest way to do what you want would be to start off with a pre-fabricated kit.
www.autoloc.com sells kits for windows, and all kinds of other custom stuff. the kits are under 200 bucks with switches, or you can add your own.
Hopefully you understand basic DC circuitry, or at least can fallow schematics well. But I'm sure if you just take your time, you'll end up with the power windows you want.
Be sure to post back and let everyone know how it turned out. I'm hoping to do the same thing to my Focus in the near future.