Hi Frog,
Important question: Do you need /want to be able to switch configurations during a musical piece? If so, you have yet another dimension of the control voltage(s) being induced or capacitively coupled to the audio circuit. The 100mv or so of the pickups doesn't give you a lot to play with for signal-to-noise ratios.
What guitar has 12 pickups, BTW??
Maybe do this differently: Put a small board with low-noise opamps like NE5534 in the instruments and feed every pickup out a cable to an external mixer / patch bay. BUT if the coils interact directly when you connect the, in series / parallel, that part would be lost.
Hmmm....