Definitely replace your fuel filter and check the pressure again, but I'm going to respectfully disagree with the other esteemed members of the forum here and say those fuel pressure readings alone are probably not cause of the engine running rough. While less than ideal, 5psi MINIMUM under full load while driving is adequate. The VP44 simply needs positive fuel pressure under all operating conditions for a long and healthy life. Having said that, I start to get nervous whenever I see pressures under 10psi in my own truck because that doesn't leave much room before a dirty fuel filter or weak lift pump can cause the fuel pressure to drop below the 5 psi danger zone.
If after changing the fuel filter the pressure is still close to 5psi under full load during a road test, then I'd definitely explore your options on correcting the problem. It could be caused by a weak lift pump or a fuel system restriction.
As far as running rough and smoking at 2000 rpm, that could be a failing VP44 or a bad injector(s). How many miles on the engine and VP44? Did this condition come on suddenly or gradually? Is the engine low on power?
Regards,
John L.