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Seriously though... Check your ignition timing, once you're sure that's set properly insert the diagnostic mode jumper firmly and go for a drive with a passenger. Have them count the flashes and jot down which codes come up. The only code which should appear is 51, that's normal. I hate to say it but if not a boost leak or AFM with damage that the ECU isn't catching it sounds a lot like knock. The Check Engine light is the only one that comes on when it stumbles? No battery or any others? That would be indicitive of a power issue. Do you have to turn off the car to get it running right again? Have you inspected the ignition components? Plugs, wires, coils, igniter?
This "it would be hesitant kinda like a boost leak then id get to speed and it will be normal" sounds exactly like a boost leak. The fact that it is intermittent is not common but does happen. A tight boost leak will only leak after a certain level of pressure is met; The "cracking pressure"... The pressure at which the leak will stop passing air again is always lower than the cracking pressure. So if you've got a leak which doesn't open until 12psi, your boost spikes to 12psi before leveling at 11psi and the leak seals at 10psi you will experience the following:
1) You accelerate and build boost normally.
2) The car stumbles when the leak opens at 12psi.
3) The wastegate stabilizes pressure at 11psi but the engine is working too hard and the ECU sees too much air coming through as the leak is still dumping air.
4) You let up and pressure drops below 10psi, the leak closes, the ECU sees that the measured airflow is back within spec and the CEL turns off.
5) You accelerate more but with caution and as the wastegate is already open there is no spike to force the leak open.... You assume all is well. You're still actually going to be leaking some air but it's a relatively benign amount.
The only problem is that this should set a code for either the AFM or turbocharger pressure. Search via Google for "DIY boost leak detector" for an inexpensive way to pressure test the system, don't exceed 15 or 16psi.
Anyway, if the CEL comes on a code will be stored 90% of the time. Only real time, non-critical codes are not stored once the detected problem is no longer evident. I'm not sure if some trouble events require a certain time period before they are set... If there are any then you may need to drive for a while before you see a code stored for that particular event.
I'm quite tired and out of it... I believe all of this is relevant to the MKIII but you might want to check back for edits tomorrow.
