Your injection pump should not be out of time. Valves out of adjustment or dirty injector nozzles could cause a rough idle. You can clean the nozzles by taking them apart and using a piece of hard wood, remove all carbon deposits.Or you can replace the whole nozzle assembly. They cost about $50/each.
Weak or worn motor mounts will cause an engine to shake more than normal.
Bill Lewallen Lexington,Ky. Where diesels purr and turbos whirr.