The intake is useless on a stock EX motor, the headers wont really hurt, I have no idea what "stock cutback" means, and a 3" muffler is way too big for a Civic (and looks ridiculous to anyone who knows about cars) but if the piping is still stock then the muffler outlet being 3" wont matter either. Whats more important is the brand of the components that were not mentioned.
Im not even going to point out the irony here..
Hahaohh s**t.. i thot that was a carpet cleaner