No luck today finding the culprit, my buddy came over and the only thing that he thought might be causing a problem was the fuel filter/water seperator combo that is under the housing of the electric primming pump. The filter showed on the directions for installation not to pre-fill the filter, so I didnt. The filter never filled up on it's own, it only got about 1/4 the way full after approx 20 hours of running. We decided to fill it up and see what happens, I dont see how it could hurt anything, I have always pre-filled any filters I change out, except air filters, LOL. I did look at that little filter on the injection pump under the fuel shut off solenoid but I couldnt get it to come out of its hole. In fear of tearing it up or getting pieces of it trapped inside the inj. pump or a injector I decided to give up on that. The fuel appears to circulate very good back into the tank with the primming pump running and the engine off, but it still seams like to me that it runs a long time before it will shut off. Not sure if thats by design or thats a clue to my problem. The update that D3DaveC is talking about has already been done when I changed mine. The Cat dealer said that they had a service bulletin out on that, but i couldnt tell any difference after I changed it to the updated version.
Maybe with presistance and some luck we might figure out whats going on. Thanks for everyones help. I will keep you updated on the status.