The only difference between the stock diagram and your wiring is that yours uses a 3-conductor shielded cable (gray) to send the pickups signals from the volume pots (white/neck pot & red/bridge pot) to the 3-way and then coming back to the output jack (black-to-black connection). In the stock diagram, the equivalent wires would be the two shielded yellow wires going to the 3-way and the shielded wire going to the jack.
Looking at the RS Modern kit on their website, you have to flip it over 180 degrees to get the proper orientation.
Looks like they're just using the Black Rose Custom wiring, but with a wire jumper instead of jumping across with the cap leg.