Don't do the up pipe.
Since you won't be doing that, it leaves you with the choices:
1. Do nothing.
2. Get an AP, use it and do nothing else.
3. Get an AP, get parts specifically supported by the AP, install the parts, use the correct AP map.
4. Get a third-party tune +/- additional parts (but again, no up pipe).
My choices would be 1, 4 without additional parts, 4 with additional parts, 2, 3 in order of preference.
Parts without CARB exemption make the car illegal on public roads in CA. Removing any emissions parts makes the car illegal anywhere in the US.