@Chris-Stratton Right, without specifying the include flags I get an error about Python.h not being found and it's nowhere in the staging directory.
Well, you can't point it at the host /usr/include, as in so doing you break most everything else.
You'll have to find the python includes for the target and point it at that.
If you configure your system build to actually build the version of python you want to use, you'd presumably have the includes. I'm not sure if they'd all be there on a the board itself, if they are you could potentially extract them back and put them somewhere.