hey guy!
i don't mean to throw a curve ball here, but...
I had the same problems that you've been describing. I even went as far as redoing a tune-up, and still had problems.
Well.. I got that 'funny feeling' about the MAE (mass air element) being dirty or broken. So I disconnected my MAC cold air induction, took out the mass air sensor part and gave it a good clean with electromotive spray cleaner ($4 or so at your local parts store). Be careful since there's a tiny sensor element which could get damaged if hit. After drying the part on the sun (and also cleaning the whole air filter assembly), I fire the car up and...bammm! no more hesitations or sputters, problem was solved.
I think what happens is that a dirty or broken sensor sends a faulty signal to the EEC causing the air/fuel ratio calculations to be offset and hence tricking the throttle body and injector performance...don;t quote me, this is just an educated guess..
Try it out, and I hope it works for you...
