It's probably a good idea to pull the plugs and check and read them to see what is going on. Also while your at it check and tighten all of the clamps(intercooler, turbo, throttle body). I would also do a seafoam treatment to top clean the engine and put the rest in your gas tank when filling up. If you have never changed your PCV then pick up a Purolator PV 1047 and put it in. And what is the condition of your air filter? Even with the factory pcm the boost delivery should not be jerky. Mine never has been since buying it brand new. You don't need a piggy back/tuner to have a great running MSP. At least that has been the case for me over the 94,000 miles that I have racked up on mine. Keep it simple and rule out the basics before spending money on unneeded parts.