Im not sure if anyone knows about this but JR radios have a DSC (Direct servo control) feature where the Trainer port connects directly to the RC receiver and controls the servos. On a JR radio, the cord is just a 1/8th mono audio cable with a signal , ground servo lead on the other end. I did some reading and it seems that the radio generates a PPM code then sends it to the RF modulator where it is sent to the Receiver and decoded back into ppm then converted to PWM. (Not sure exactly though) So if this guy in the URL can feed a PPM signal into a radio to control it, then you might be able to use the JR DSC feature to directly control the receiver with only two wires!
http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1193927390
Would that code work with a JR radio by the way? I think it would if they were both on the same shift, just not sure what pin to hook up to what on the arduino. From the code it looks like only pin 12 is used and the rest are power or not used?