Not sure if you have a turbo charged diesel?
If your turbo seals are toast it will feed the engine "oil" which it will actually run on for a little bit and cause the run away symptoms you are talking about. If you do have a turbo equipped truck check for play in the turbo impeller shaft, and if there is any oil in your intercooler hoses.
Diesels have no spark, so they will run on oil, so check to see (if you don't have a turbo truck) if there is oil getting into the intake somehow. Leaky injectors will also over fuel an engine.
Beyond that, I don't know much about the old 6.9 diesels, I can tell you anything you need to know about the 7.3, 6.0 and 6.4 though
