5.9 cummins wont run right after injection pump replaced
 

My boat has a 5.9 mechanical cummins in it. My injection pump had a failure and was taking to a professional for rebuild. After installation and bleeding the lines the motor will run, like crap, but appears only the #1 cylinder is actually carrying the load. When you give it fuel it dies. When running and cracking injectors, only when you crack #1 does the motor slow down, the others don't have much or any response when cracked. We thought it was air still in the lines so we bleed them for over an hour nothing really changed at all. When bleeding the fuel appears to have bubbles in it. I am not sure if that is air or just from being pressurized and spitting out? We timed it at tdc with the pin behind the pump on the motor and the pump was also set at tdc with the pin in it, witch we took out and flipped after everything was set. if it was out of time, but #1 is running good, then i would think one other cylinder would have to be running well as well. Someone mentioned that my injectors could have gotten stuff in them when the pump failed, if it spit some crap through the lines?

Any help or thoughts is greatly appreciated.

Thanks,
Capt. Greg