Truck Repair: excessive smoke, rotary pumps, excessive smoke

Question
We have a Cummins BTAA5.9C engine in a JCB front end loader.
Bosch Rotary Injector pump was leaking/spraying fuel out side cover. Went to have pump rebuilt as suggested by Cummins and the pump people said the housing was corroded and warranty would be limited. Purchased new pump and installed as outlined in Cummins Manual. Engine ran for over 30 minutes and we shut down to install side panels. Went to start engine again and we have excessive smoke coming from exhaust. We think we may have a timing problem. But why would it run great for 30 minutes?  

Answer
Rotary pumps should have a key in the shaft to go into the fuel pump drive gear.Remove the plug on the frt to gain access to the fuel pump gear nut.It should have around 1/4" of threads protruding past the nut.If not,remove nut & look for the key in the keyway of the gear.