I finally have the ground station (gs) talking to the brain (raspberry pi) and the io_board (crius/avr). I get sensor data, can calibrate the accelerometer/gyro/compass, send uav and camera input and so on.
The io_board sends sensor data at 500Hz to the brain and also runs a rate PID at 250Hz. Motors are mixed on the io_board using a throttle input from the brain.
The brain will do AHRS at 500Hz using the sensor data from the io_board and it forwards data to the gs at 30Hz.
The next step is to get the io_board simulation working again to be able to test the rate pid, stability pid, motor mixer and GS.