Do you have a wideband meter? My car would do that sometimes on the original revision of my tune. AFRs would drop to the bottom of the meter and the engine would sputter because it was getting flooded with gas. Your starter only comes into play when starting the car, never (hopefully) while its running. I'm @ 5kish miles on mine now with the stock starter and no issues.
I think that a real tune will help you. If you bought the kit new, definitely call Stillen, if not I would say get in touch with a local tuner and get it done right. Sebastian @ SpecialtyZ does most of the Stillen A2A guys' tune, but I imagine he could be a great help to you too.
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