Easiest and safest performance mod though, is the TRD S/C. Will get you decent power, and make you happy if used to it being N/A. Bang for buck, get the URD S/C. $2k plus more, but out of the box, between 80-100 whp more than the TRD out of the box.
Make sure that you get mods, that will work with future mods, so you don't spend money twice.
The new Doug Thorley headers will work with all setups. Good investment. 304 stainless steel. Catbacks don't gain you much, except sound, unless you do custom stuff.
Fuel pump is always a good upgrade.
The new style trd intake is not the way to go. The Afe stage 2 I believe is the old style TRD, and that is the one that you want. Especially if you get the TRD S/C.