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Some times my '97 PSD when I start it only runs on about half of the cylinders. I have to shut it off and re start it and it normally runs fine. Some times it takes 2 or 3 starts to run right. After it is started it runs fine.
Bad under valve cover wiring harness. 100% guaranteed! You are lucky if it runs right for now, but I guarantee you that the day will come when it won't, and then it will only run on 4 cylinders.
Let it run for a little when it does this and check the exhaust manifolds to see which side is getting warm. This way you know which valve cover to remove, as it will be the side that is still cold.
Basically, the IDM will shut down one whole bank of cylinders whenever the injector resistances are out of spec to protect itself. Shutting off and restarting the truck may fix the problem breifly, if the resistance is close enough to the specs that it may not cause a shut down the second time. Usually you will need one valve cover gasket and at least one set of injector/gp wiring harness that goes under the cover.
Let it run for a little when it does this and check the exhaust manifolds to see which side is getting warm. This way you know which valve cover to remove, as it will be the side that is still cold.
I second that one. That's one of the best troubleshooting tools I've ever known. I'll bet that it's the same cylinders that fail every time.