Thank you all for your comments.
As was mentioned, this is a carb'd bike so any power commanders are out. The only option is a full exhaust (very few available) or slip on (Two Brothers M2), air filter (K&N), and the re-jet. The YZF600R is more of a Sport Tourer than an R6 or CBR600 or Gixxer 600. Those are pure race set bikes. The re-jet kits are only available in a Stage 1 for my bike. The Stage 1 is basically for stock or slightly modified pipes (slip on) using the stock air box and filter or an aftermarket kilter such as a K&N. The Kit includes jets for the stock filter or the aftermarket. The filter claims gains, the pipe claims gains (weight loss and performance gain), and the re-jet claims 5% with the Stage 1 kit. 5% on 80 (HP guesstimate) isn't much HP in a car but can be big gains on a bike, or so I have read. Same is true with TQ which we all know is where it's at. Even 1 ft/lb can be noticed.
As said, I am a complete noob when it comes to bikes and am trying to get as much info together before diving in.