With the CR toploader 4 spd and a final drive of 3.54. 1st gear, still gets you 60 mph. IMHO, I am looking for those catapult hole shots. With 500+ lbs. of torque, you will have a problem getting traction out of the hole. The 3.31 or 3.08 will help with the traction problems. With a 3.08, you will still get a pretty good acceleration, but it will be aggravating in parking lots and traffic, not to mention the wear and tear on your clutch. Just my opinion.
http://www.secondstrike.com/Technical/GearCalc.asp http://www.368s.com/tools_rpm.php
There are a couple of websites to help you out. Hope that makes your choices a little less complicated.
Here is some original specs of the 427 Cobra, 3.54 final drive and a CR toploader. These look pretty good to me!
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"The 427 Cobra is easily the highest performance car ever sold for street use. A decent 427 - not the worst, not the best, will go from zero to 100 mph and back down again to zero in less than 14 seconds. All thing considered, you can put together a pretty good argument that the 427 Cobra is the ultimate performance car, judged on any basis you want to name." Taken from; Corvette, The Sensuous American