I had exactly the same issue with a Duncan Distortion a while back. Everything measured correctly, wiring correct but the output was too low. It turned up it was the pickup height. I had to put it too close to the strings and that solved it. I don't know why but, it's still a mystery to me. And it happened with two duncan distortions, not one. I was hitting repeatedly the low string E of my warmoth strat with an Alt8 and was getting 160mV and the distortion that's supposed to be hotter was giving 60mV. I had it raised a lot closer than the Alt8 to get a similar result. Anyway now with the Painkiller and normal pickup height, it gives 300 - 400mV....lol.