6.1 Swap Won't Rev Past 3K HELLLLPPPPP!!!

I wonder.... you are using the 5 speed manual ecm. How are you handling the clutch start bypass? My assumption is it is grounded across to allow start up. Is this correct? If it is doesn't this give the ecm the believe that the clutch is disengaged at all times? If the ecm thinks the clutch is depressed is it possible that the neutral rev limited is set at/near 3000 rpm?
~Michael