The best way to come out on top of the road's little surprises is to make sure you're riding with the best posture. First off, keep your toes on the foot pegs - riding flatfooted means that a bump can unseat you and your control of the bike. Staying on your toes lets your legs act as a secondary suspension system for your body. Second, make a good, strong connection with your
lower body - squeeze the tank with your legs so that you could even take your hands off the handlebars if you wanted. On our ninjas I've found that the 'default seat position' puts your knees where the body is narrowest and makes it hard to squeeze because your legs are already so close together, so I like to 'choke up' on the bike and scoot forward to get a better connection. You'll find that it helps to have a little more between your legs (and the ladies love it, too

arty). Finally, keep a mantra in your head that goes, 'light on the bars, light on the bars,' - imagine floating your hands around the grips and only give steering inputs by pushing with one hand (try to avoid pulling).
Shazam! The next time you hit a bump or pothole leaned over in a corner, you'll still feel the bike 'shudder' or handlebars shake slightly, but since you're not resting on them you won't give them any further-destabilizing input. You'll feel the bike move under you, but your head and torso should just glide along like nothing happened. This technique, of course, works great in straight lines too - just try riding 4th street between Gilman & Virginia to test it out!
Enjoy the smoothness!
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By the way, are you the guy I've seen around town on the blue '06 with black helmet & sweatshirt?