The fact that the LEDs are different (the color code is similar actually) shouldn't matter. Nevertheless, we'll get this clarified for you in our docs next week.
Assuming that the parts you purchased are valid and work properly, feeding a PPMSUM signal into the PXFmini will get you set up. There're several ways to debug the incoming PPM signal into the PXFmini. A simple one is to hook a scope into the signal.
You can also place some traces in the RCInput code and verify that the values obtained from the receiver are appropriate (this will require that you recompile the binary of the autopilot). A similar thing could be done using the ROS interfaces (look for
Let us know how it goes. We'd be happy walking you supporting your build.