My university has been experimenting with their own flight controller for some time now. It's got pretty solid airplane control and simple copter control (angle and rate mode), but for the time being we can't create a Kalman filter to get good position and altitude estimates.
As a stopgap, I want to suggest using a Pixhawk board & sensors running ArduCopter to provide lat, lon, alt, hdg, v_x, v_y, v_z, and # satellites to our controller. Will this work? Beyond configuring the board, doing all of the normal calibrations, and getting the data out, are there any gotchas I need to be aware of? Does the board need to be armed to avoid any sort of state changes or resets?