Hello,
I am not that familiar with Futaba, But I'll take a stab at it. The "cord" that comes with AFPD is USB on one end & 3.5 mini (phono) on the other end. This fits JR transmitters with no adapter needed. AFPD also comes with an adapter to adapt the stereo phono plug to many other transmitters. This adapter is 3.5 female jack on one end, then it "Y's" out into two plugs that I think are DIN. They look similar to a PS2 mouse plug but larger. Neither one has six pins though. Both have 5 pins. If you compared this to looking at the lug bolts on a truck axle, one would be a six lug axle with the bottom lug bolt missing. The other one looks like a ten bolt axle with all five bottom bolts missing. In both cases the line up notch is straight down. The Commander version gives you a simple transmitter, similar to a buddy box in case you don't have a "real" transmitter but would like to fly the simulator. I hope this helps.
Crowfly