Air in the lines is a big problem, if you changed the injector pump did you change out the fuel filter.....
Also what is the specs on the pump; new, used, run with bio diesel with older seals, run with low sulfur diesel.....
Also do you have a clear line running from the filter to the pump, maybe you have air rushing in through there...
check all lines to the fuel filter, there is no way to know unless everything is checked
I have a small leak on my return line but it runs into the fule filter, I ma leaking air in there, and after a hard run at night, in the morning, the car starts roughly, until the air get's out of the pump.