Have you run sudo apt-get dist-upgrade? The newest release has the fix for the motors’ issue. Skim through the threads attached to this post. I’m pretty sure your problem may also be fixed with the upgrade.
I am sure X8R can not handle 16 channels through ppm, only through sbus. Should not be a problem though, Navio2 can handle both.
Passthrough only works 1 to 1, so to act on output 9, you have to use channel 9 from your TX/RX.
If I am not mistaken, there should be a landing gear function in the RC_X_Function list. This way APM will control the landing gear automatically.