Do you guys still have the egr valve hooked up? Sometimes the diesel doesn't like the hot gasses going into the intake. It will make it smoke at slow engine speeds after engine warms up. From what you have discribed sounds like thats what is happening.
Bill

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94 dodge cummings,86 ford 6.9,75 mbz 240d[ sold], 82 mbz 300sd,83 mbz 300sd