You could try and upload your tune again to the EMU, but running without one should just make it be like stock (I think).
Have you checked to two LED lights on the side of the EMU, how do they behave with ignition on and when you try to start?
From the EMU manual:

ACTIVE L.E.D
• Steady GREEN - - - - - - When the unit recognize Ignition ON
• Flashing GREEN - - - - - When Fouled Plug feature is activated (When engine
is started with wide open throttle)
• Quick Flashing RED - - - - When Self Diagnostic has detected an error
• Flashing RED - - - - - - - When Warning is activated
• Flashing Orange - - - - - During Main Unit Data Logging

INTERACTION L.E.D.
• Steady - - - - - - - - - - When the unit recognize Ignition ON
• Slow Flash - - - - - - - - When confirming engine rpm
• Flashing - - - - - - - - - When communicating with PC