My .02 worth.....
Gears: Go 4:10 and stick with Ford Racing. I've heard very few people regret going with 4:10 with the 3v. If your going to boost it, you could go with a lower gear, but 4:10 will work fine with boost as well (just have to have a light foot in 1st gear)
Bracing: Yes, you can always improve bracing, but as mentioned above, the 10 are pretty stiff and I would spend my money on other components first. You won't see as dramatic of a change with bracing as you would on say a fox-body.
CAI: There are 2 types of CAI. Those that require a tune and those that do not. Do not waste your money or time on a CAI that does not require a tune. The reason for a tune is that the computer on the 05+ cars are much more tightly regulated than on previous generation Mustangs. They simply will not accept (safely) a better flowing CAI without retuning the computer. Therefore, if the CAI does not require a tune, it is really not doing much more than stock (or worse is letting your engine run lean). A tune will also improve your throttle response (drive-by-wire) and a host of other changes (speedometer correction for example).
For tuner-CAIs, there is not a lot of difference. Steeda, C&L, JLM are all good brands. Get a quality tuner. 2 that come to mind are Breenspeed and Bamachips. Bamachips has just recently joined with AM, so I beleive the tunes you get from them are Bamachip tunes.
Brakes: Well, the faster you get on the track, the more you hate your brakes. If your an occasional auto-x/track runner, then upgrade the lines and pads. After that, the sky is the limit. Why upgrade brakes over more HP? Better brakes will allow you to go into the corners deeper. Better brakes will allow you to run more than 2-3 hard laps without brake fade.
A couple of items you did not mention and to consider. Shocks/struts, springs, CC plates, adj Panhard bar. Why suspension? It is going to allow you to be flatter and more predictable in the corners. That combined with improved brakes will allow you to enter and exit the corner faster. Exiting the corner with a higher speed will allow you to get a higher speed on the straight-away.
Exhaust: If your not wanting to get LT, then just upgrade the axle-back mufflers. They are the real bottleneck in the exhaust system.
Tires: Pretty well covered above.
Superchargers: I am not an expert on SC. Have you looked into the Ford Racing roots? I think that can be installed and retain factory warranty. I do know a little about Prochargers and the stock engine will take something like a P1SC fine. Good for street and auto-x, but if your going on the bigger tracks, be prepared for heat-soak issues.
Not to take anything away from HP improvements, but I've seen many times where a lesser horsepower car with better brakes and suspension out-run/turn better lap times than higher HP cars on a road/auto-x course.