It's not just as simple as opening up the breathing. If it were, why would runner length be such an issue? We would all have box intakes. By having too big of a throttle body, you are reducing your air velocity and, therefore, the momentum of the air moving into your plenum. With less momentum, you get less of a bounce in the runners, and less air being bounced into the cylinders. You do, by the way, get more into your cylinders than you would if you just let the cylinders suck air into them without an intake.
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351W 89 Mustang GT Convertible