I am very interested with the way you are ''deconstructing'' the APM, Modularity is the key to integrate with ROS philosophy and to attain a high level of agility and redundancy.
I noticed that you already using a PWM module in the system.
Are you planning to integrate the PPM as a NODE in the near future ?
If so, it would be very interesting to have the opportunity to connect the transmitter via USB to the base station (either a PC or a BBB Router) and uplink the PPM stream (published on rostopic) to the Drone via the WIFI (actually it could XML over a UDP port or a dedicated rostopic channel ?).
The transmitter radio could be used as a backup link to the vehicule and the Autopilot Node would be a subscriber of both channels-topic (PPM input on the cape AND XML command over WIFI)
Seems to me to be a natural evolution for yout teleoperating module, what do you think ?