If the header is Cali legal, you can get a cali legal aftermarket catalytic converter installed and be covered there.
The mesh breather is part of the PCV system. You need to check if your aftermarket intake has provisions for the PCV valve.
Your best bet to making it legal, if you don't care about performance upgrades, is to trade/sell that aftermarket intake for the stuff you need. (Stock intake, PCV system, and maybe some help installing it properly.)
I believe the PCV issue can also effect the EGR code, but I'm not sure about it.
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