I had exactly the same problem - this is the document you are looking for https://www.dropbox.com/s/1rzjsxzrzx8onf9/PixHawk%202%20Connector%20Pinout%20-%20Leo%20Technologies.pdf?dl=0
I ended up cutting and re-soldering the cables rather than trying to change the connector on either cable
Pretty sure it was the 4 & 5 cables that were not needed
Thx