Isuzu 4ZE1 engine miss.

G'day from Australia I have an Isuzu 4ZE1 in my ute (pick up). Marketed here as a Holden Rodeo but maybe some Chevy or something where you are? Any way it has developed a miss. Very uneven and jerky driving at low speeds. Seems to be ok when under full load or fast highway speeds but terrible when driven around town. I have replaced, the spark plugs, leads, fuel filter, and air filter element. Nothing made any difference. I have since replaced the engine (I cooked the other one). I fitted a rebuilt long motor which means I had to swap over all the manifolds etc. Problem is the same, although I have more torque now. New motor against one that had done 440,000 km would explain that bit. I don't know much about fuel injected petrol engines. I work on heavy vehicle diesels most of the time. Should I be looking at the injectors or the MAF sensor or what?