Its a seal issue, probably leaking at the pump head or the front shaft. A leaking pump head really wont affect how it runs all that much, however a leaking shaft seal will really mess with it, by alowing air to get into the pump and turning the fuel to a frothy mix. Try running the pump from a jar of diesel fuel held above the pump so it gravity feeds it. If it smooths out, you know the pump seal is sucking air and thats your problem. Also check or replace your fuel filter if it hasn't been done recently, a partially clogged fuel filter will also lead to poor performance. I would try those and get back to us.
Jason
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