nothing you do will cost less then trading your bike for an r1...so when the money is an issue you really cannot put major hp's by modifying your bike...
i hear a lot that changing your counter sprocket is the cheapest mod that will make a difference on your acceleration,,,by going down one tooth you will loose some high speed but you will get there a little bit quicker...
spend another $1000,,you get exhaust+power commander+air filter...
then still its no r6....
if you dump thousands of dollars you could put a turbo kit and/or nos,,,,they will blow your engine real fast but hey you'll be the fastest fz6 out there...
these mods are all about the power,,,,by upgrading your suspension and taking an advanced riding course you will learn to get more out of your standard FZ6....
and as lots of us here would advise,,,,if you are trying to put major hp's to your bike,,,simply just buy a couple year old r1..