Some people run into charging or cooling issues when using the underdrive pullies. however, I have all 3 pullies on my set up and have no problems. At idle, the alternator puts out a little less than normal, but I have never had any problems starting the car or anything. My battery still charges up fine.
I wouldn't spend your money on a throttle body right now. I don't think you would notice a thing.
Also, I have the Gt-40 crate motor in mine, which uses the same heads as your Cobra (GT-40 irons). I am getting the power in my sig. with a B-cam, GT-40 intake, and all the usual bolt ons, including TB and MAF. That may just give you a little idea about what you might want to do with your combo.
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2006 Mustang GT
1990 LX
GT-40 motor 262 horsepower, 307ft-lbs (sold but forever loved)
1998 Contour SVT
Rice Haters Club Member #244
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