I had exactly the same problem and the best I’ve been able to come up with is this patchwork here.
For the moment it works, but I’ll probably buy some “native” Pixhawk 2.1 modules, as soon as I found them.
I’ve found Pixhawk 2 cable pinout here: https://www.dropbox.com/s/1rzjsxzrzx8onf9/PixHawk%202%20Connector%20Pinout%20-%20Leo%20Technologies.pdf?dl=0