Get a header, and cut out the cats. You said you've already got a new muffler, so i wouldn't bother replacing the entire exhust system, unless you want duels, but thats more for show then anything.
After that, I wouldn't put any more money into it because your not going to be getting very much in return. If you have the tools, you could pull off the intake and clean up the ports a little bit. Then you could pull off the head and clean up the exhust and intake ports and stuff a new cam in it, But really for the amount of power your going to get from any of those (or them all together) it isn't worth your time. I'd just fix up the exhust and save up your money after that for maybe a nice set of rims, some suspension parts or a paint job or something.