I see what you mean. Better to have tried and failed than to have wondered what if. 
I think I may default to using a stereo cable instead of mono. I'm trying to make something that would be easy to incorporate into guitars without much circuitry. Thought I'd try if it would just be something simple like a cap in line, you know?
But as for the stereo cable, I just need to make a sensing circuit for the pedalboard so it will stop supplying 9v power to the 2nd lead on the cable if a mono is plugged in. In this way, if the 1/4" stereo plug is used with a mono cable, the 2nd lug will connect to ground. I haven't decided on which method I may use: Use arduino to sense current, resistance, or voltage(I think voltage may be the easiest), or to just use a relay that will switch itself given the ground signal returns 9v, and then it will sustain itself there, then when powered off it will reset itself, or along the lines of that..
Can't really think of much else than that.
But if I used the arduino's analog input to determine the voltage(with a voltage divider of course), would the AC signal hurt the input if only for a short moment? I would like to not use an inductor if possible, unwanted distortion and low freq. loss through the arduino to ground.
But onto the communication/wireless. I picked up 4 nrf24l01+'s on ebay for <$8, so my evil idea is to communicate the ardy's with a pair(1 on pedalboard, 1 on guitar) and then transmit that directly on the audio wire rather than air. I just wonder, from the theory you have taught me thus far, I could run the 2.4ghz signal over the audio lines and the +9v line, without issue, right? Or would I be better off running it on the ground line?
Now for the possibly crazy idea. For wireless, run that into another pair of nrf24l01+'s, but with an antenna. I don't know how I would go about amplifying that signal just yet though. Off to google I go!