Where are you getting a supercharger kit that adds 170 horsepower???
I'm betting that the supercharger didn't make 490 on a otherwise stock engine. How much boost will you be running. I would do some other mods before I threw on a blower. The flowing mods should help you optimize your combination.
1)3.55 or 3.73 gears
2)full exhaust(headers, off-road X-pipe, 2 1/2 cat-back)
3)larger mass-air meter and a larger throdel body
These are just basic mods that I think you should do. But I feel the exhast is a MUST HAVE!!!
As for the extra power I feel that the stock transmission should hold up, bri32Z is running high 10's in the 1/4 mile with a stock T-5. The new transmissions in the Cobras are stronger than the T-5's or T-45's. If you deside to go with a different transmission I suggest a TKO. Also your IRS rear syspension may not be up to the task of all the extra horsepower(although I've heard that SVT has made many improvements to it in the area of durabilaty since the 99 Cobra debued), especially on a drag strip with sticky tires. I would look into swaping in a solid rear axle from a 99-02 GT(which should be beefed up).