IdleSam:
Do you think I am over-complicating the issue?
Yes... 
really just listen for the serial port for the time being
if you want to sleep your arduino - then what you can do is indeed have an ISR on pin 2 but make that just wake up the UNO, then read a command and when the command is handled, go back to sleep. Don't mix the "wake up call" with reading the data from within the ISR. (and you are likely going to empty your Serial buffer faster than you receive data.. so your way of handling serial is not great --> you should study Serial Input Basics)