Good question about break in. I know how hard it was for me to break mine in with the 4K limit for the first 500 miles. I think that came out to be almost 55MPH in 6th gear. Then 6K for the next 500 miles. I also topped of my oil with some Myster Oil, and used a half of quart of Mystery Oil with every oil change until recently. Now I use Castrol Syntec Blend. So far, no probs and the engine still pulls strong.
I did the break in as recommended by the manual. I also read on a website when I bought the bike, that this method produced the least amount of engine wear during the break in period. Tha site took two new engines and broke one in using Kawi's method and the other their own way. At 1,000 miles, they disassembled the engines and inspected the wear. The one broken in using Kawi's method had less wear. I'd post a link to the page, but it's been 3 years. I don't know if it's still around.
I know some Ninja 500R pages come and go quick. They used to have a company that made a 600cc,700cc, and 800cc Over Bore & Stroke Kit for the 500R. Can't find that site at all since last year. The worst part was they sold a ton of race parts for the bike.