The GT-40 will work well. It makes a lot of torque. Some of the other, newer intakes make more top end power but less low end torque. People generally only pay attention to the peak hp number and nothing below that.
I believe the best long runner intake available right now is the Holley systemax.
A 65 mm throttle body will do just fine.
FWIW, I run a GT-40 intake and a 65mm Motorsport throttle body.
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1988 Mustang GT
11.8 @ 123 (7/14/01)
1992 BadAzz Wrangler
1993 Explorer
See my car at:
www.mustangworks.com/cgi-bin/moi-display.cgi?179