There is nothing rider skill can do about it. In gears 1-3, there is nothing you can do to make the bike any quicker, besides aerodynamic or suspension changes.
More power, more aggressive gearing, none of it will do anything. The bike already has more power than it can use. In fact the argument can be made that the changes you made actually made the bike slower to accelerate. You increased torque to the pavement, which increases the bike's tendency to lift. As well all know traction control doesn't take only what it has to, it overreacts, takes too much, then gives it back, etc.
As for accelerating faster through 4-6, the sprocket changes will overall make a negligible difference in torque to the pavement at those gears, and you'll have to click to 5th quicker, at which time until 5th has matured the OE bike is putting more torque down.
The changes you made are all in your head. Sure if it was a Honda Civic or Ninja 250 they'd do wonders, but this bike has more power than the chassis can handle.
In the US we have Top Fuel drag cars. With 5,000hp and a normal car weight. Would you believe me if I told you adding 2,000hp would actually slow them down? They already spin the tires down the entire length of the quarter mile. What they need is more traction.