Hello Jon,
If your vehicle has a lot of miles on it, it could be the EGR valve, not opening and closing properly. Over time carbon builts up internally,some models have a diaphragm in them and works up and down on a shaft inside the unit, I've cleaned this in the past, remove and disassemble (usually not complicated to do), and either clean gasket and/or replace it. Other systems. have only a solenoid or two, which can also become restricted with carbon. This is worth a check, you stated that it was coughing and spuddering at low revs--EGR problems can have your symptoms as well as lack of power, if EGR is not working correctly it can be either symptom.
EGRs can set computer codes also, if you have access to a Code Reader this may help also.
Hope this helps,
In Christ,
Walt, October 2008