Sounds like it might be sucking air. Did you use the hand primer when you changed either of the filters? If you still have the "screw top" primer, change it. When they go bad, they allow air into the fuel system.

If it were my car, I'd make absolutely sure I had bubble-free fuel at the injectors before doing anything else.

Jay.

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On the road, currently:
'83 300D (German spec.) 168k mi. - - Wolfgang (tucked snugly away for the winter!)
'87 300D 375k mi. - finally went over to "The Dark Side"
'87 300TD 225k mi.
Cannondale 66cm CAAD5 w/Campy/Jamis Aurora
Hujsak Custom Fixie/Landshark Track Shark Custom/Ahearne Custom 29'er