Did the ISC sync yesterday. It seemed strange to me that the ISC seemed to act the same whether or not the diagnostic tool was set to sync mode. The adjust mode requires that the bike is at operating temperature and it was taking forever. It also acted a little strange just as it crossed the line with the temperature jumping back and forth (likely as the thermostat opened the extra cold radiator water dropped it a bunch?). Anyway, the imbalance was significant and when the test mode would autocancel itself due to engine temp being low, nothing noticeably changed. Maybe it was too far whacked out for it to compensate. I suspect that it doesn't adjust balance but only tries to correct the idle speed which was very low on my bike. Maybe it was at the edge of its adjustment there. Strange thing was that when it turned itself off and I turned it back on it didn't seem to affect anything.
Regardless the balance not only significantly off, but the natural idle was only about 800rpm. Just on the cusp of stalling out. I had to open both idle air jets to get the idle rpm up to the prescribed 1229 with a perfect vacuum balance. I don't know why they spec 1229 rpm since the numbers bounce all over and you can only estimate the average to be about where you want it... Reset the learned position and reset my throttle position sensor (which was also off).
I only had time to run around the block a few times. The low end struggle was MUCH improved; however, the engine was still partially warm so I'll have to confirm on a completely cold start.
As expected the engine vibes at rpm didn't go away. They may have shifted a little bit, but I'll have to get on the freeway to know if anything is better up there. If the vibes moved into the 7k+ instead of the 5k+ then I'll be good. It is the speed limits of 80mph+ that put my bike right in the buzz rpms when cruising all day.
One final note... I've never heard of a new bike having as much trouble as yours (especially the burned valves), but I will say that all of these factory adjustments on mine have been way out of whack. All the exhaust valves had the same size shim in them as did all of the intake valves. Maybe that is normal mass production technique but it seems that they just loaded them in based on design tolerances and never actually measured them. The odds that they all turned out exactly the same based on actual measurements seems to be pretty low.
The throttle cables were completely wrong too. I thought I would have to adjust the cables at the throttle bodies to be out of spec to get the upper adjuster back in the middle instead of with only one or two threads engaged. But when I got down in there they were nowhere near factory spec and fixed up fine following the procedure in the service manual.
And my idle circuits were not only imbalanced but very low. This may have been ordinary wear in change, but I've always experienced the cold engine, low rpm, barely cracked throttle struggle to turn its own weight phenomenon. Which I suspect was not normal despite the dealer shop's line of BS that started with "you're not warming it up long enough" and headed towards its normal and ended with me never going back there for service.
The bike has been great despite needing the tweaks mentioned above, so hopefully your new dealer experience will turn out for the best and you'll be able to enjoy your bike for many years to come.