After spending the day taking a ride on the Ninja 500, I noticed a lot of things I typically don't on my commute that I usually take to work.
For one, the engine feels much more broken-in at this point. I went for a night ride about a month or so ago. It was chilly, which allowed for good temperature range for the engine break-in process. I properly heat soaked the engine, went through the full rpm range, and maintained working temps to fully seat the piston rings. It showed tremendous difference in the engine. What used to be jerky when lifting off the throttle is smoother, more linear. The cylinder walls were not properly broken in up to that point, so it's extremely noticeable when working in the power band. Paired with the Quick Turn Throttle(QTT) Tube by TST Industries I installed, it improved both acceleration and deacceleration by reducing throttle rotation. The sensitivity and responsiveness went up significantly. The engine is still bone-stock beyond the Yoshimura slip-on exhaust I installed.
Two, my own comfort level on the bike continues to grow, but I'm still maintaining a level of tension and discipline. I have my "big boy" bike(Yamaha YZF-R9), yet I chose to take out the Ninja 500. Main reason being, for defined purpose. It's a different bike for a different mindset, it offers a different set of expectations, accommodations and enjoyment. I still appreciate both in it's entirety and that's something I myself give credit for, for being able to fine tune my own expectations for 2 different sport bikes.
Overall, my experience as a motorcyclist continues to help me grow as a person. With each ride, I try to have something to take away from to add to the collection of memories for my own untold biography.
I'm looking forward to installing the Hindle straight pipe and getting an ECU flash which is still being planned. This will be the biggest upgrade to date on the bike so I am quite excited(and nervous) about it.
Below is an article regarding the engine break-in process. A good read for a bit more info regarding it. I myself went by feel and instinct because of my own experience with cars and other motorized vehicles, but your mileage may vary:

Engine Builder Magazine
How to Break-In Your Piston Rings, The Right Way! - Engine Builder Magazine
One way to ensure the horsepower built into your engine is achieved is to seal that cylinder pressure on the push side of the pistons.