Fuel delivery problem, could be:
1. Injection pump failing
2. Dirty injectors
3. Bad fuel (try a biocide in the tank and change the fuel filter)
I think you ruled out the other fuel delivery problems already. Did you notice any stains below from a diesel leak from the pump? The top seal on this pump tends to leak, it is the seal between the top 1/3 and bottom 2/3 of the pump held together with allen bolts. While in park rev and set you hand throttle a 3000 RPM this helps expose any leak while its under high pressure. Use a flash light to check around the seal.