In my opinion the cabling problems with Ardupilot are significant and not due to Ardupilot itself. Because it is open source hardware vendors can/have changed the connectors freely leading to a real mess. That is one reason I am such a fan of canbus.
To speak to the problem at hand I posted a request to update the documentation here with a diagram of the pin-outs of the Pix2.1 carrier because it is hard to find on the net and not available here.
It is posted in my request under general | doumentation changes and gives you the power pinouts to hack your own cable up which is generally the only solution. You can purchase a high current version with the right cable for pix 2.1 from Chris Mauch.