For some strange reason I am having two cylinders run lean and two run rich specifically 1-3 lean, 2-4 rich. I have tried new coilpacks, and just recently went back to stock injectors. I even tried a different wiring harness for the fuel injectors. This problem is really weird, could it possibly be a megasquirt issue?

 

Are they set up in batch fire?
with the ms you can make the adjustments.
are you reading the plugs to see what's lean and rich?

 

More data. What injectors? Were they flow tested? How do you know that you are rich / lean on a cylinder-specific basis? Idle, part throttle, full throttle? Did the problem occur with the non-stock, or the stock injectors? What Megasquirt? Post your tune. What car? What Mods?