Is this on a Turbo? I replaced and adjusted the rack bolt on my injector pump. It is the little bolt on the rear of the pump near the bottom. Several (thank you by the way) advisors on this forum told me to replace that bolt, and after adjusting several times, it has made a world of difference. I don't know if the non-turbo's used them, but I'm sure you'll get more very informed responses.
Also, if you haven't, run some Red-Line Diesel Catalyst through...you'll LOVE the results.