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You will have to tune for the headers so you can tune out AFM mode at the same time. That will prevent the engine from running in V4 mode but that won't prevent the CEL for disconnecting the AFM acutator.
I believe HP Tuners has a way to tune out the AFM valve check but it is in the body control module (BCM) and not the ECM or TCM. It costs more points to tune that module. I believe many people use the method below.
The AFM exhaust valve is two pieces. The actuator motor connects to the wire harness and is bolted to the actual valve in the exhaust. You can unbolt the actuator and leave it connected to the wire harness to eliminate the CEL while removing the AFM exhaust valve. Just carefully tie the actuator up to the bottom of the car someplace where it won't be damaged.
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