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3. Potentiometers were not supported in the moment by MobiFlight, so you should look for an alternate Produkt like BU0836A from Leo Bodnar (USB Interface - http://www.leobodnar.com )
But if you intend to make the radios specifically the adjustment of the frequencies or the transponder-code then your a right with encoders. Encoder are supported by MobiFlight.
I almost have al I am needing to continue but can anyone tell more why running Arduino and mobiflight? More god argument why I should invest in arduino and mobiflight!