Thanks for the response. Here's some more info; We have a new Area Rep, the last one moved on, I understand he's down in Atlanta now. (try not to deal with this clown, hasn't got a clue) Anyway the new Rep shows up to see if he can hear the noise. He calls me and says he can't hear anything wrong, maybe it's just loose clearances. He also suggested I get the bike back, I hadn't really ridden it since the repair. I did as he asked, picked up the bike, road it for a week and took it back. It definetly knocks on startup, and gets quieter as the engine warms up. The guys at the dealership have been great, the service manager said he knew I'd be back, he had heard the noise himself. Anyway, the manager told me he was surprised Honda had let the new Rep come back to my bike, seems it's got something to do with legal stuff. Anyway this time he heard the noise, and now he's going to try and get a sound bite to send to the engineers again. I don't know where we go from here, the manager at the dealership has suggested I get a lawyer, he even gave me a name, it turns out Maryland has a pretty good lemon law, who knew. My bike has now been in the shop 7 times for engine noise. I'll try and keep you posted. Message to the two responses I got, on the engine teardown, the guy at the dealership told me the bearings were the first thing they checked, he then told me how Honda fixes this problem. They replace the bad parts the then peen the cases to prevent the bearing race from moving again. Not the greatest solution. As for the tapping, the service guys checked the fuel injection system as well. Little know fact, the Rune engine actually fires their fuel injectors in triples, so the chances of you hearing one injector making noise is really low. Stay with the dealer on the ticking, these engines should not tick at all. Mine really only got bad when the ambient temps went up, like June in DC. (90+ degrees) then it got really loud. I wonder how much longer my dealer will be willing to work on my bike, Honda now owes them in excess of $2K for work already done and hasn't shown any interest in paying that either.
PS I'd love to bring it down to SC, but it's still in the shop and I'm not sure what condition it's in right now.