It sounds like you have a fuel restriction. Start at the line that runs out of the tank to the filter. When you open the tank valve you should have a full flow of fuel from that line( steady stream, no dribbling). If you don't, than I'd suspect you fuel strainer is clogged or the tank vent is restricted. For a temprary fix if it's not the vent, blow back through the line to the tank with compressed air. The real fix is to pull the tank valve and drain the crap and corruption out of the tank.
If you have full flow, reconnect the line and check for low through the filter. if you had good flow going in and poor flow at the outlet , the filters is the problem or the internal supply passage in the filter body is clogged.
If you have a lift pump that provides some boost to the fuel injection pump, they often have a filter screen and that could be clogged. often you will have to bleed the pump once you have run out of fuel. You manual should tell you how to do that. I have some general bleeding intructions that work for most diesels. if you need that let me know and I'll post it.