As far as I know the only difference on the CA models is the inclusion of a charcoal canister in front of the swingarm. Instead of the fuel tank vent and overflow hoses routing to the ground, they go into this charcoal canister. This is supposed to absorb fuel vapors or any overfilled fuel and keep it out of the atmosphere. Since it's just the vents it has absolutely ZERO impact on performance so there's no point removing it, maybe just to save a half pound of weight, that's all.
My blue 05 bike has it intact. My silver 01 bike was purchased in Indiana then later registered in CA so it doesn't have the canister. There's no difference in performance between the two bikes.
CA models also have different carburetor part numbers but I don't know the differences; maybe it's just different (leaner?) jetting for CA? Irrelevant if you install a jet kit.
The airbox mod is only beneficial if you rejet the carb, which you should do since you mentioned you have an aftermarket exhaust. The Ivans or Dale's (holeshot) kits are very convenient, but the RavenRider carb mods are significantly cheaper. Only downside is sourcing all the parts separately. It's much easier just to pay upfront and have a full jet kit.