I'll temper this by stating that my local riding conditions include pretty crappy roads, and have a big influence on my suspension opinions. So, keep my bias in mind! Id start out by trying a lower seat, and lower the suspension as only a last resort. It's basically mathematically impossible to shorten your shocks/forks without compromising the suspension performance/ride quality. Sorry if I offend with that statement. Granted a high quality shorter suspension setup may be "better than stock". That's due to the factory air shocks and damper tube forks being cheap crap to start with. Take a ride on good quality shocks/forks at stock height, and then try the short version of the same shock. You'll feel the difference. BTDT. The only way to keep a short shock from bottoming out is stiffer springs=rougher ride. One advantage you have, if you do have to go with a shorter suspension, is being shorter also generally means that you weigh less, which will help offset the shorter travel. Also, if going the short shock route, get the very best shocks you can afford.
2009 Vivid Black FLTR/120R/Dewey's headwork/TMan 625G/Fuel Moto XXX 2/1/2 w/4" mufflers/HPI 55