I wouldn't pull the motor apart, it really sounds like a tuning issue. Check plugs, see how they are burning, rich or lean? If they are uneven, then you might have to pull it apart, if they are all lean or all rich it's probablly tuning. Make sure your map and tps sensor are functioning correctly. Your tps should be at .45v at 0 throttle. Check your ignition timing and fuel pressure as well, fuel pressure should be around 50psi usually.
You also need to check your af ratios. You really shouldn't even think about pulling the motor apart before you check all this man. You'll save your self a lot of time and money.