With a sustainer, I'd stay away from the Custom/59. It's a great pickup, but it doesn't have perfect hum cancellation. Not an issue for most uses, but sustainers want no hum and higher output pickups.
P-Rails is a great choice if you want flexibility, though it likely wont work terribly well split with the sustainer on. Serial should work fine, though. Most sustainers automatically switch to bridge serial humbucking anyways because of noise issues and need for high drive for maximum sustain. Parallel might work noisewise, though the lower volume compared to serial might not give optimal drive for sustain.
JB and Full Shred are also great choices. Might also look at PATB-1b [high output, but very dynamic pickup], but you'll likely need the pickup routes enlarged. But where you mention the body is being built, that shouldn't be an issue.
Would really need a better description of what you are looking for tonewise from the guitar, to specify a particular pickup.