First off, you might want to try it without the Tornado for comparison. Disconnect your battery for 30 minutes after pulling it out or putting it in, and do some real driving both ways.
A custom ram air hood is something that'* been discussed before. I personally think it'* a great idea. Speedguy is your tranny mod dude, and either him or angry duck will be the source for the CAI (you're right about what it means
Your exhaust? You'll do fine just taking it in to a muffler shop, and tell 'em what you want. Nobody makes a bolt-on for the Bonnie.....yet.