Generally the 'bare' wires are all earths and the others are signal from the pickups. So you just need to track your signal path to the output jack and make sure every thing that needs to be earthed is. Most wiring can be done a number of different ways, but the PDf should be the most common.
From what I've read I think this is part of the wiring. I saw somewhere that I can connect the small black wire and the ground wire together. Is that correct?