As someone who went through this EXACT same issue just last week, here is what I suggest. Change the fuel filters again (my issue was caused by a bad spin on fuel filter I had bought and used for only about a week)!

If the filters do not fix it, try this in order

1. Clean the filter screen in the fuel tank
2. Blow (or flush) out the lines between the tank and the injection pump
3. Check all fuel line connections for leaks and look for air bubbles in any lines (both static and with the engine running)
4. Adjust the valves

This should set you up right. Please let us know how it goes

__________________
2012 Mercedes ML350 Bluetec 102K (hers)
2005 Corvette 55K (fun car)
2002 VW Jetta TDI 238K (mine)
1998 Volvo S70 T5 Turbo 211K (kids)
1994 Ford F150 4WD 246K (firewood hauler)
1983 Mercedes 300D 384K (diesel commuter)