Hesitation, pausing while accelerating

While accelerating mainly around 1.75-2.75 rpm's the engine hesitates/pauses then accelerates more then pauses again, after 2.75 rpm's is reached there is no problem.

Recent work done: transmission flush and filter, harmonic balancer, idler pulleys, belts, water pump and timing belt, mass airflow sensor, knock sensor, valve cover gaskets, spark plugs, wires, distributor cap and rotor, fuel pump, fuel filter, fuel pump relay.

Original transmission and engine.