If it were my Brute, I'd stay stock. Reason being is I've had my fill of buying all those aftermarket hop-up parts, constantly tinkering with the machine, and all that with that ZX-7 roadrace bike I mentioned earlier. The only modifications I've done to my '07 Brute is a Moose Module, Warn XT30 winch, Warn ProVantage plow, 26" Swamplites on black ITP SS-108 wheels. It does everything I want it too and I don't have to constantly tinker with it to keep it running.
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2007 Brute 750i
Warn XT-30 Winch
Warn Pro-Vantage front mounted plow
26 Swamplites on 12" black SS108 rims (9" frt, 12" rear)
Fender Flares
Oil Cooler
If it were me, I would run with a stock crank and rods, but install aftermarket high compression pistons and some aftermarket cams. Your going to have to "tinker" with the jetting after if its carb'd or buy a fuel controler to dial that in properly, but your going to have one hell of a power increase.