To disable the PAIR, doing the entire mod, you'd need to remove it, and block off the valves and the holes in the airbox. When I had my 929 custom mapped, the tuner blocked it off by pinching the hoses closed with some hemostats. That works fine, just make sure the tuner does it. That is, unless you're planning on doing the PAIR mod anyway, then do it prior. I have the valve block off plates from Dan Kyle, I've just never bothered to do the mod.
Doing it won't add more power, but, if after the installation of a full system and map if there's popping on decel, removing the PAIR will remedy that.