little history on the car.
2006 Mustang GT
BBK 62mm throttle (recently installed)
Edelbrock Shorty headers (recently installed)
K&N Cold Air Intake (it came with it when i bough it used last year)
Running Good on (Stock)
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Later
Ordred (Ebay Bought) Steeda Cold Air Intake
Ordered SCT Tuner (free tunes for life, 91 street 91 Performance 91 race)
When ordering SCT Tune it gave me an option of 80mm or 90mm Steeda CAI, I guessed and chose 90mm, to go along with the tunes.
Check Engine light came on but not right away, CARMD tells me to replace MAF (Mass Air Flow).
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So I switched back to K&N CAI, and Stock Settings SCT. No Check Engine light.
Here is a pic if my steeda is 80mm or 90mm

if Im rights what could be wrong, because at stock and K&N CAI its running normal.

 

Why don't you measure it? Try to get a diff tune with the 80mm CAI option.

You also might want to clean your MAF.

 

Get new tunes written specifically for the Steeda CAI and also let them know about the TB. It's most likely the incorrect MAF size for the CAI in your present tune. If you still get the CEL, then install the stock TB. You're not seeing any gains with the BBK TB unless you're FI or internally modded.