Pulsing/surging during hard acceleration

Hello, my car is surging, pulsing or hesitating during moderate acceleration (merging on to highway, overtaking slower vehicle). It starts doing it around 3,000 rpm's all the way to 5,000 rpm's. I have read a couple posts from people saying that it is the fuel filter but I cannot seem to find a parts store that carries one. AutoZone said that it was not serviceable. Another post said that it could possibly be the fuel pump, however the car runs great. I just had the engine rebuilt about five months ago and it only has about 3,000 miles on it since rebuild. I am pretty handy when it comes to cars but this one I am stumped.