Do you know of issues with the missing Ch2-Ch1 input option with the Line6 Mobile In and/or iPod touch 5G combination ?
I have seen that sometimes, the difference channel (Ch2-Ch1) doesn't show up in the input channel list when using the hardware you mentioned (iPod touch 5, Mobile In, Lightning adapter). It should work however, if you restart the app and reconnect the Mobile In. I'm still not sure exactly what the issue is that causes this behavior.
Would using a power amplifier be advisable to take some current load off the iPod/iPhone/iPad headphone output ?
You could use an amplifier. You could also increase the size of your series resistor (8.2 ohms is pretty low).
Are you aware of any iPhone/iPod/iPad compatible USB input devices that have floating inputs ?
Perhaps, you could look for a digital input device and use a separate piece of hardware to handle your analog signals.
Ben