Try this:
./waf configure --board="pixhawk1"
./waf sub
It will say the build directory before finishing, in my case it was /home/will/git/ardupilot/build/Pixhawk1
Choose “custom firmware” in QGC:
And the firmware file will be in the /bin directory of the build folder, in my case
/home/will/git/ardupilot/build/Pixhawk1/bin/ardusub.apj