Okay. The "whine" that you are referring to is the true trademark of supercharging. The K&N that you installed eliminated all the blockage points in your intake system. This includes the resonators that dampen the whine of your supercharger. Everytime that you open up your intake or exhaust system you will increase the level of noise that can be heard in the engine. The resonators in place in your X were there for this reason. Actually, the Roots style supercharger on the X is quieter than a centrifugal supercharger found in most bolt-on kits for cars.
Everytime you add a performance tool it affects driveability. A high lift cam will affect a vehicle's idle, in your case, the K&N opened up air to the engine and you are getting the feed back from the intake.
Personally, nothing sounds better than the whine of a supercharger working happily under the hood. If the wife and kids ask, I would tell them that is the sound of power.