I am new to a r6 I had a 99 750 SS full fairing. The bike had all of the first line of updates, slip ons, air filter and so on.
After 100 ft. on my 04 r6 I knew the r6 was 100 times better bike than the Ducati. I will never own a Ducati again, parts are expensive and limited in upgrades.
So my first question is this. what can I do to get alittle more grunt out of my bike. I already have a Yoshi pipe. Is a K&N air filter the way to go? Also who has carbon fiber at a "fair" price?
One more thing....these r6s are nice bikes.

For more grunt I'd go with a 520 conversion on the chain with a 15/50 set up and a BMC Race filter (stock fliters flow better than K&N on the R6).

As for the Carbon....OPP Racing is the best bet. You can try GYT (Genuine Yamaga Tuning) but some people say the quality is suspect. OPP has everything, all fairings, even a carbon tank if you wanted. If you want a carbon part OPP is almost guarantee'd to have it. www.oppracing.com.

I like Duk's and would own one if I had the $$$. They are totally different than the R6...but I like em.

No I don't think you would want a Ducati. The build quality is always suspect and it is a nightmare to fix. The twin cam bike need sevive every 6k or 5 years and it is very expensive. If you have a belt break who knows what it will cost to get it fixed if the parts are even around. The dealers kill you on the parts because it is a Ducati and they are not very confrontable. Take it from a guy who has been there.....don't go there.
If I get a new air filter what will that do to the air/fuel mixture? Will I need a power comander or will I be able to get by?

Since you were asking about Filters I assume you already have an exhaust, at least a slipon. If you don't a filter will do little to nothing. If you are serious about some more power a full exhaust is the only way to go. With the full exhaust you will NEED a power commander. If you do just a slipon and BMC filter you can get away with the #29 wire mod to richen the bike up.

dyzak, where would I get the chain sprocket set up you talked about and how much should it run? Remember, I am an ex-Ducati driver and the price of parts is all over the place w/Ducati.

520 conversion kits can be found as a set at like ebay, just be cautious what gearing they sell you and who makes it.
Sprockets, stick with like sprocket specialists or vortex. If the pro's use'em they're probably good. Fronts should be like $16 rears $30-$40 depending on how many teeth.
Chains again stick with big name o-ring or x-ring jobs. D.I.D, RK Chains, again stick with top names. You don't want like the Cheng Shin of chains or sprockets because it'll be crap. (Cheng Shin makes like $25 sportbike tires that suck real bad)
You'll be getting a 120 link chain that you'll probably have to cut down to 116 or 114, again depending on what size sprockets you get.

Oh and chains will run $85-$125+. They have a wider range depending on what you get.
I run DID race x-ring. It's more expensive then a regular x-ring chain but it's thinner and lighter. Light=acceleration but also light=crappy longevity.
Also x-rings are supposed to be better than o-rings, because on the seal, the ring itself there is an extra groove that holds more grease when you assemble the chain. More grease is always better.
Good thing with a 600 is they don't produce huge amounts of power to the point where you're blowing chains all the time. A superbike would stretch a race chain over the course of an event weekend or even a single race depending on who's at the stick. But I can usually get a chain to last a summer of am racing if I keep it oiled and clean.