(this is coming from a COBB user) Go with the JB4 -- Since you're concerned about heavily modding your car because of CA's emissions laws, it doesn't sound like you'd go FBO b/c of DPs.
Going with the JB4, it'll allow you to take advantage of not only the Auto-Tune feature (the car basically makes a custom tune to the mods you have installed & quality of fuel you're using), BUT you'll also get to take advantage of E85 fuel. E85 is becoming the big thing & it'll give you a really nice power increase over standard pump gas.
IIRC, the Injen intake is approved for CA usage. I don't believe that any of the DCIs (BMS, ETS, aFe, etc), so that might be the only "affordable" intake that's okay for CA usage.
Exhaust, go with the BMW PE. It's an axle-back exhaust but will give you a great change in the sound, allows you to continue to use manufacturer quality parts & remain compliant with CA laws. There are a couple other axle-backs you could consider like the Akrapovic Slip-On, Billy Boat, Eisenmann, Remus, Rogue Engineering and UUC/Corsa