It's not a no load tone pot is it? If the pot is no-load and you wire to the wrong lug, the tone pot won't work, and when you wire to the middle, you'll get the wah tone again.
I would start by checking all grounds, making sure everything is in phase, and then try wiring both the jack and the selector to the opposite (left or right) lug on the tone pot, maybe you got that backwards? Remember, you're looking at the pots upside down. A volume pot will still work if wired backwards, the taper would be wrong, but a no-load tone pot wouldn't work at all.