My comments are based on the similar break-in limits for the Kawasaki 500R: From many sources I found the recommendation that break-in (always with a well-warmed-up bike, including idling it a couple minutes following shut-offs, even if you were gone a couple minutes, to assure oil distribution) should include:
Riding under different speeds and loads, a mix of street and highway, a little steady running, but a LOT of variation. As, I think HOMER said, not to keep it at a steady highway run for extended miles.
And, to assure a good "mate" among all meshing surfaces, a lot of Wide Open Throttle (WOT)acceleration. This does NOT mean exceeding the R.P.M. limits, but rather putting load on the parts during acceleration. I was such a newbie, and so timid, that I did almost no WOT during early break-in, and I think my reward was a grumbly drive train. Once I developed some skill and confidence, and began grip the tank, hang on, and to TWIST! that throttle, the bike appears to have smoothed out some. The hard acceleration seems to be a healthy thing for the mating parts.
ALSO: do not switch to a super-slick, or synthetic oil during break-in period. It will inhibit the (oiled) pressing together of parts that must form to one another for best operation. After a strong break-in, you may wish to change to another oil, but use "standard" motorcycle oil during break-in. (Synthetics are not ideal in all situations.) In the old days, when synthetics were new on the market, they supposedly could cause leakage in some engines. I recall a Popular Mechanics, or somesuch, auto-advice column which cautioned that synthetics would not induce the swelling of engine seals and gaskets that standard oils were formulated to do, or that the seals wouldn't "absorb" the synthetic well, so the seals could leak. This was in regard to a Honda car question, as I recall.
Yes, the break-in lengths of 500 and 1000 miles are annoying, but plan a few long rides that will cover a lot of non-highway miles. (I did a few 350- 375 mile weekends)You'll get to develop skill in your shifting, get familiar with the bike under a lot of conditions, etc., and get to do a lot of accelerations from stops. I don't know about the 6R, but the 500R owners' manual has ridiculous shift "speeds" that keep the bike in a grumbly, lugging range. It gives incredible gas mileage (I got 74 mpg once) but is miserable. I now run it in the 4,000 - 5,000+ rpm range and the bike is much happier. And those WOT's are a blast. This little Ninja can fly!
"Abandon All Sloth, Ye Who Enter Here!"
It is just not possible to keep it under 4000 for 1000km. Period. Anyone who says otherwise is either lying or is just not cut out for a sport bike 
