I did exactly what the Seymour Duncan diagram told me to do.
Neck pup = Black - ground. Yellow top control, soldered to the same spot I cut the other from. Bridge pup black - ground, blue soldered to same spot I snipped the other wire from. And of course grounding the pickup to the claw.
I kept the bridge pup in the box as I worked on the neck pup, triple checked that I was working with the right pup before I started.
I don't think it's the wrong way around. Two black wires on each pup, unlike the yellow and blue, so I'm pretty sure black = ground, as also indicated by the diagram. Which is what I did...
I like the switching the switch idea. Like I said, it sounds perfect, just, backwards compared to how it was functioning before.