On my last carb bike, an '81 GS1100EX, I put on individual K&N pods thinking it would make it runs faster. Well not too much, it kinda ran like crap, but I stuck with it. Keep in mind this was 20 years ago, no dynos, jet kits, nothing. All we had was a "plug check". Keepin mind that from '80 to about '83 that bike was the "Busa of the day, and with my filters I was running with 750's. Pride can be a problem at times...
One of the problems I had was in cross winds. The bike leaned out so much if hardly ran. After struggling with fueling for a year+ I put the stock air box back on and it ran like a champ! Man did I kick myself in the butt for wasting so much time with a poor running bike.
The FZ600 motor really runs with nice with hi-comp pistons and high lift cams, but I don't think filters will help you.