The diagrams were created when the stock pickups were only two-wire, but the factory has recently started shipping 4/5 wire pickups. Normally, the following would be the layout:
Black = hot
Red + white = series link between coils (leave them joined and just insulate the ends if you're not coil splitting)
Green + bare = ground (and shield)

However, from your post it seems things are different again. Your description would suggest: white = hot, red/green = series link, and black/bare = ground. But, just to be certain, can you upload an image of the pickup wires and confirm they are the stock kit pickups.