I couldn't see a cold air intake hurting anything, but depending on what size exhaust you put on your car you may not be able to compensate for any torque you may have lost. Opening up the intake, installing a bigger camshaft, putting on new exhaust, etc., all change the power band and engine airflow/resonance and put torque higher in the RPM band (more top end/horsepower), if the airflow of the engine doesn't match you can actually lose power or have less noticable power at lower rpm's. What size exhaust did you have installed?
If you get a higher ratio axle gear set you can get your engine in the power band faster and you'll feel a huge improvement in acceleration.
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2005 Suzuki Hayabusa GSX1300-R
1980 Ford Thunderbird - 255 V8
ported heads, 5.0L ported stock headers, O.R. H-pipe and Flowmaster 2-chambers, dual roller timing chain
hi-po Mack Truck hood emblem
1985 Mustang GT 5.0L T5, F-303, GT40p, headers, off-road h, flowmasters, MSD stuff, etc.
Sold 02/06/04 
1989 Mustang GT ET: 13.304@102.29 mph (5-24-03)
Sold - 1998 Mustang Cobra coupe, 1/4 mile - street tires: 13.843@103.41 (bone stock)
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