Start cheap, and then work your way up.
If your fans aren't turning on, chances are it's the switch, it's a $15 part and easy enough to change. I doubt it would be the control module since they tend not to go bad w/ the frequency as say the switch would.
Auxilary water pump wouldn't case overheating since it runs after the car's turned off. If it's busted, you'll hear a nasty, almost grinding noise coming from it.
Make sure you're not leakin' coolant too.
Good luck w/ it.