In my past experience, when ever you make a car that came from the factory N/A into an F/I set up, it always leads to problems of 1 kind or another. Hell, even cars that come from the factory F/I have issues, coughSTiandcough. Also, even without taking F/I into consideration...the more power you add over stock the more issues will want to pop up, weather it be engine, transmission, diff., ect. related.
Just my 2 cents
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