Have you tried switching your pup wires on the 3-way? I thought I had a problem with my TL-1 so I tried wiring the neck pup to the bridge location on the 3-way switch. It at least proved that there was nothing wrong with my pups. Turned out all the noise and dead bridge pup was the result of wiring the output jack backwards.
Can you post a pic of your output jack wiring?