I don't know about Cali, but where I am in Eastern PA if the car is a '96 or newer (with OBDII port) they just check for codes. No code, you pass emissions. Other than Inspection considerations it's up to you, but the new Jpipe will need a custom tune which can be pricey. Every tuner I've spoken to says the CVT can barely handle the stock 2.0DIT's power / vehicle weight, but I haven't broken mine yet. I thought I did, but it looks like it was a vacuum leak and computer issue. I hope!
Go to your inspection station and tell them you're considering a custom tune and exhaust. Ask what is and isn't an issue for inspection. That's what I did.