I don't know first hand what the kit comes with. When I did mine, I purchased my plenum plate from a guy over on thespeedfreaks.net. I sourced my gaskets and everything else separately. I see you're going to do the thermostat. That's good. I'd also recommend doing the coolant bypass hose. Other than that, I can't think of much. I know a lot of guys say don't reuse the intake bolts. I did. I don't think it's an issue to reuse them, but then again, I'm not responsible for your vehicle.
01 TJ - 4.0L, NV3550, 2" Skyjacker budget boost, Xenon flat flares, LoD front bumper, Tuff Stuff rear bumper, RH4X4 sliders, 33" STT Pros on 15x8s