If i install new headers, air filter and muffler would it effect the particle admission coming out of the car?
If you leave all of the emissions systems intact and operational emissions should remain the same and in some cases they have improved.
What emissions system would be affect by replacing these things?
O2 and catalyst systems, IAT system. But as I stated if you do not change any of these but leave them where they are with no modifications then emissions will remain the same. If you start modifying components then you will have to have you ECM reprogrammed for the mods.
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