Sod to the whole 'what's a custom builder bullsheet!' Matt, you do good work. If you want to pay for your electrics to be done, hell, why not. Does one person in PRS make the whole guitar, finish it, wire it and set it up. Sheet no! Does it make it any less of a machine? No! Giv it up fellas.
Matt - when they have rewired, what have they actually done, rewired or replaced components?
If they replaced components, did they replace tone capacitors etc too? Break down the circuit into parts and see what hasn't been changed yet. You could also just try another pickup off another guitar onto the circuit and hold it over the strings or maybe do th same with this pick up over another guitar.
It may be worth taking the pick up out, wiring a jack socket to it direct and just trying that through an amp.