Obviously I'm going to have to reverse the wiring since the middle pickup is wound backwards,
Don't reverse the connections to compensate for winding direction. Black is still ground, white is still hot. The middle pickup is reverse wound, but it also has reverse polarity on the magnets. The reverse polarity magnets cause the string to generate a signal that is out of phase. The reverse winding causes the signal to be out of phase. It's a "double reverse". So the net result is: in phase.
Where did you get Eric Johnson pickups? Fender doesn't sell them separately from the Eric Johnson guitar. You might want to check the part number to determine if these are actually EJ pickups.
Yeah, I had the same worries, but the guy had some solid reviews and the pickups sounded great (plus I did notice he was selling one of just about every other EJ Strat part). It's got the sticker on it, I just never tried to verify it in any way.