You shouldn't have to worry about overheating/ECU issues, that was on the 05. That problem was largely mitigated on 06.
I agree you should make sure the front brake is working well. If it's stock, it's ok, but it really (ideally) would be upgraded. Again, not expensive for you to do this yourself.
The main issues with the 06 are front brake as mentioned, and 2nd gear. Make sure it shifts into 2nd cleanly, and doesn't pop out if you hit the throttle hard in 2nd gear.
I agree with those that talk about starting cold and making sure the oil is filled correctly. If overfull, the 06 can blow a rod out the case.
Take a look at the clip-ons where they fasten to the bottom of the upper triple clamp. If the screw that holds them in place is gone, likely the bike has been down, as those screws get busted out when that happens.
Make sure the full-lock pegs are straight. These are on the bottom triple clamp. If they're bent, welded, or gone, it's been down hard.
Other places I'd look for damage are the fairing stay mounts (in the nose, holds up the rearview mirrors), the speedo and speedo mount, and the ram air (the plastic piece that holds all those up). See if there are any cracks or if it's all loose or the ram air is drooping. Not a deal breaker, but heads up the ram air is about $90 if it's busted.
I bought my 06 used in cosmetically rough condition, but with 9k miles on it, we jumped it and it started and warmed up nice, so I knew the engine was good.
Never ride faster than you can stop