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you need to check your A/F ratio. with the added air from the throttle body, it may be running a little lean, so if your gonna do it, i'd suggest getting a dyno tune, unless you have a wideband. but definately check your a/f.
yes it does, i have a SCT Xcal 3 tuner and i just put a bbk 65 twin on my 97 cobra and it is bolted to a C&L cold air with K&N Filter and C&L Mass air and it worked perfect, but idle hanged a litttle but fixed it with the tuner, works awesome and i can feel a difference.!!
How did you fix the hang up with a tuner? Which option?