The clean air system admits air through the exhaust port outlets into exhaust system, and has no effect on the engine... I have sealed off the air suction valve on the valve cover with 1/4" aluminum plate, and the air source on the airbox with RTV silicone. I also removed the air switching valve unit by connecting its two wires together to prevent triggering the 'FI' warning light.
This is common practice when installing an aftermarket exhaust silencer. I have a Muzzy header with custom Magnaflow 2" in/out, 2.5" core silencer and Yoshimura TEC-SD2 1-7/16" ID 'low volume insert'. I also smooth matched the exhaust port outlets, among other things.
No such concerns about leaning out the overly rich stock Versys/Ninja 650R. The slightly lean ~2800 rpm range is there stock or with a slip-on, and progressively too rich, especially beyond 5000 rpm. Fuel injected engines are normally completely leaned out on maximum deceleration (closed throttle). That and/or admitting air into exhaust reduces emissions, and also submits less strain on the catalytic converter in the stock Versys muffler...
I pulled this Invader quote out from another post which was already rather highjacked as it was and didn't want to add unnecessarily to it.
The question I have regarding this mod is, rather than fashion a plate,
jumper a wire, and plug the air box port, shouldn't you be able to simply plug the airbox port to the valve and just leave it all in place as
factory installed and get the same result? That result being no air routed from the airbox thru the valve.