Linkage! Looks like everything was mentioned with the exception of the throttle linkage. Make sure that when you have the petal to the metal that the pump linkage is at the full throttle stop. Inspect this by pushing the pedal down slowly to see if it works properly. These engines do tend to be a little doggy for the first couple of minutes (mine included) but after a mile or two I have full acceleration from my '85 300DT (230k mi).

This is just a single piece of the puzzle and you want everything working as designed....

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