I have a 2002 Grand Prix GT 3

I have a 2002 Grand Prix GT 3.8L. Just had the upper plenum and lower intake gaskets replaced, the valve gaskets replaced, a new EGR valve, a new radiator, new plugs and wires, and a new 4th gear shaft put in my transmission as the car was not shifting from 3rd to overdrive (this works fine now). The problem I have is that sometimes when I am in the middle of accelerating from a stop or as I am driving up an incline and slowly accelerate to maintain power, the car starts to accelerate in a very jerky or choppy way. I am usually depressing the gas pedal 1/4 to 1/2 way. The RPMs go back and forth from 1500 to 2500 as this is happening. But if I punch on the gas, the car will accelerate faster and not do this. It does not do it constantly. But it does happen every time I drive. My buddy is a mechanic for 20 years and he is the one who did all the work above. But he too has no clue what is causing this and is stumped. Ideas? It is driving me nuts!