Just unplug the window switches and see if you have a draw. If that is the culprit then install a relay that's pwr'd when the key is on and allows the existing circuit to pwr the windows etc......
My bet is that the alt pig tail has been crossed, my reasoning:
The draw of the lights in the switches shouldn't draw the batt down that much (unless the battery's starting to go bad)
When you lay your hand on the alt caseing is it warm?
Terminal #1 from the alt goes to the one side of the idiot light on the dash. The other side of the idiot light goes to a switched 12v source (hot when the key is in the run position) This is the exciter wire and tells the alt to start producing juice. The idiot light does not get a ground wire, it gets a ground from the internal regulator in the alt when the alt isn't spinning. That's why it lights when the key is turned to run but the engine isn't running, and it goes out when the engine starts.
Terminal #2 from the alt goes to the hot side of the wiring system, normally itís spliced into the hot feed leading to the fuse box. This is the sense wire, it tells the alt to produce more or less juice depending on the demands of your electrical system.
So if you switched them, the hot side of the elec system is grounding via the internal regulator and will drain your battery in 2-3 days.