I'll clarify, I used the method on this page I'm linking to.
https://www.fjr1300.info/breakin.html
Yamaha's break in instructions are still followed by this method. Also Minuscule shavings in a brand new engine is usually normal, reading a lot of other posts.
Really I am asking about the idle problem, this has been there since pulling out of the dealer lot (thought it was me learning the new clutch feel) it has only been 5 days.
Also does the oil overfill mean anything to this? other than they really are morons....
FWIW mine was overfilled too. Seemed like some lightweight oil too. Seems to shift better with a 15/40 in it. No idle or stumbling problems with my 08.