1) Good choice. Can't really get a BAD CAI, but don't expect to get 30 HP and 3 MPG from it. They truely are more for looks and sound. Although they will help some, I have an aFe stage two. S&B makes a cool one for your truck
2) A muffler is a muffler..doesn't matter what truck it goes on. A billion guys on this site run magnaflows. Keep with your flowmaster, they sound better anyway in my opinion. People will say the straight-through design of the magnaflow is better performance wise than flowmaster but I dont think it's a huge difference.
3) A lot of guys run JBA, I think BBK is another company.
4) Might as well do the y-pipe too while you are at it.
No matter what you get, we have an AWESOME vendor here on this forum called Discount Auto Performance, run by Jeremiah and Andrew. Their contact info is below, they will set you up with the best deal around on any of these items. Well not sure about headers and AEM actually, but doesn't hurt to ask.