Diesel Bombers - duramax disgusted--HELP

I am working on an 06 C5500 Chevy. Just put a new high pressure injector pump on it due to a fractured ceramic valve internal to pump and lost fuel rail pressure. I now have adequate fuel rail pressure but, the engine still has a hard to no start problem without a shot of either. Once started it runs perfectly until it is driven about 2 miles and then goes into a "limp" or "safe" mode and then will not turn over 2250 rpm. There are absolutely no DTC's in the system. Datastream shows all sensors to be operating perfectly and the only oddity that I have noticed is that the scan tool showing "PTO engine shutdown" is on or enabled. The PTO switch is not on when this happens but is exactly how the vehicle acts when it does show this message. The vehicle is totally stock and is driving me crazy. If anyone knows what could cause this Please helpl