Unable to calibrate radio (megapirateng 3.0.1 r4)

Hello everyone
I have to design an autonomous flying quadcopter(including follow me mode) similar to iris+ for my graduation project. only thing is the quad has to arm, hover, follow land and disarm itself when it receives a call signal from a user(instead of using a radio controller, user is going to have an x-bee module and some function buttons). Since we had a limited budget, we bought a crius AIOP v2 clone and decided to use megapirate firmware. For the first flight, we decided to fly it with a radio(frsky fs9x) to do calibrations and PID settings. First I used the flash tool and it worked well(I was able to do radio calibration) however it allows us for limited operation(unable to set aux channels for stabilize,follow me mode etc.) when I uploaded the mpng 3.0.1 r4 code from arducopter arduino 1.0.3 and changed ppm enable to ppm disable line of the RCinput_MPNG from eclipse c++ I couldnt able to do radio calibrations. I tried all megapirate codes with mission planner(latest version) but couldnt understand what the problem was. What could be the problem in this situation? Do you suggest any different firmware solutions to this project? I would appreciate for any help.