Hi remington,
I want the arduino to generate a 125 kHz square wave first. Once that is outputted at some pin, I want to read that very signal approximately in the middle of the wave but not the edges. This is taking into account of the jitter. In real time, the square wave will contain some data superimposed on it. So reading it in the middle will help obtain that superimposed data(assumption - I m aware for this a separate analog circuitry is required). Does this make sense?
I am unable to even serial.print to the serial monitor. It's printing just the first two characters of the string. 
Best,
AM