New '06 VFR800 owner - Questions

New on this site after buying my son's 2006 VRF800. I changed all the fluids and filters. Switched out KN filter with KN that came with bike which had greater filter area. Bike was previously tuned with the old kn filter and power commander. With the new KN the bike sound rough. Should I re-jet the bike or switch back to more restrictive filter? Also, are there any old timer HONDA mechanics in SW Missouri or NW Arkansas that can check the valves and systems? Bike only has 25,000 miles on it..

Thanks!