No, you can't test a capacitor that way as the multimeter will use a DC voltage for testing and a capacitor only passes AC. It's very unlikely it's a bad capacitor, so it must be something else.
A close-up photo of the wiring would help.
Also, with two tone controls and three pickups, how exactly have you wired them up? If it's just like a Strat, then you won't get any tone control operating on the bridge pickup - a standard Strat doesn't. You can modify the wiring so that either you have one tone control shared between two pickups, or you can leave the middle pickup without a tone and have it on the two humbuckers. Or leave it as it is and have the bridge pickup without a tone control.