As @
Anthony mentioned, intake, exhaust and tune will help, but also getting rid of rotational mass. Light weight Crank, light weight flywheel, carbon fiber drive shaft, light weight wheels and gears are going to be the best bang for your buck if you want to stay NA. You won't have the actual horse power to back it up, but the car is going to rev faster (and get up to speed faster) and a lighter car is always a good thing.
I'm not planning on doing much to my car, but this would be the rout I would do if I get bitten by the mod bug. I've owned a couple factory supercharged cobras and heat was ALWAYS an issue.