Best thing you can do is the Shoodaben ECU flash. That will give you much better rideability at lower rpms (below about 4000), which will translate to much more fun. I think it is also advertised as giving more torque and hp, but jmho those things are immaterial unless you are literally racing/tracking your bike. Having a bit more low rpm torque and better throttle accuracy will make it more responsive as you initiate acceleration. Once you get to about 6000 rpm the engine really comes to life, so if you want max power then you should be operating in the 6000-9000 rpm range.
If you want more acceleration, change the sprocket ratios. If you want more top speed, concentrate on aerodynamics (hint: windshield). For darned sure put better tires on it!
Changing out the air filter may provide more airflow, but again the increase in hp is not likely to be measurable in real world riding.
Reducing weight on the bike will help performance. Reducing the weight of the wheel assemblies has twice the value as reducing dead weight from the frame. Lighter brake disks, lighter wheels, lighter tires, lighter sprockets. Even a lighter chain.
But really all of that is only going to make a measurable difference in balls-to-the-wall full throttle acceleration or in race conditions on a track. The mission of the V650 is something different than that.
I have read everyone rave about the 650 ECU flash and had my '18 done last year. i can feel no difference in the engine at all. I thought at first a mistake had been made and the ECU had accidentally not been flashed at all but I know it had because the fan runs more. I had another bike flashed by Superbike Unlimited last year also and was very pleased with the results from them.
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