Be aware that even with humbuckers or any other type of "noiseless" pickups that if the wires you run to the output jack aren't shielded, you're going to get a surprising amount of hum. With single coils, fuhgeddaboudit. They're always noisy.
Alligator clips are very handy for testing wiring schemes and control functionality, but not so much for finding noise problems as they generally pick up quite a bit of noise themselves.