Tough MotorCycle Break In Process?

Hey, I just bought a brand new 2016 Honda CBR500R fresh out of the crate, i'm close to 500km and I have been riding it pretty hard (full throttle, improper gear shifting like from 5-1 without releasing the clutch, shifted without the clutch a couple of times, and sometimes not letting the bike warm up before riding), I just figured out about the break in process and the oil change at 1000km, i'm scared this might cause some damage to the bike and how long it will last. I have noticed the shifting getting soft to where I can't feel shifts, and the braking has softened up a lot as well. I figured the engines would be tested in the factory and alreading broken in but i'm and idiot.
Added (1). What happens to an improper motorcycle break in?
Added (2). What happens to an improper motorcycle break in?

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