I may be wrong but a K&N filter alone does not make a Stage 1. You can get a K&N filter element for the stock AC (the filter has a rectangular shape with rounded corners) - and then there's the K&N filter element for the SE Stage 1 AC which is oval in shape.

 

Just how bad of a surge is it? I had the same feeling but not like riding a bucking bronco, but more like some one was trying to do it doggie style to the rear of the bike. I have a 2007 1200C with a stage one exhaust and a/c and found that after I hooked up a set of X14iED's all that went away. Just saying.

 

A K&N is still a "high Flow" air filter so i would think it would the change air flow.