Surprised to hear about the chain wear. Good job dealing with that. Would you please measure elongation per the service manual procedure and post the results here? I'd like to know if the manuals procedure accurately assess the wear present in the chain, or if there are other types of wear in the system.
As for your top end break in process, most folks around here subscribe to a more aggressive break in methodology. The rings need load in order to seat into the cylinder wall, and babying around during the break in defeats that purpose. Here is one such methodology that has gained wide acceptance...http://www.mototuneusa.com/break_in_secrets.htm Personally, I think that method is a little extreme, but the idea being to load the engine from the beginning and not go too easy is good. Aggressive riding using a city driving cycle works perfectly. Lots of engine load, no lugging. Vary the throttle position and rpm. After 50 miles or so of that get out on the highway and do some pulls to further load the engine. All this is well covered in the archives in older threads around here. You might want to do some more research (if it's not too late) to educate yourself.
Good luck
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