The difference in colour probably points to a different exhaust temperature. This may be indicative of a problem, but then again I've also heard that even in normal operation the cylinder temps can be markedly different. A failed O2 sensor would certainly lead to abnormal running (the bike may revert to a 'get you home' ECU map - I would have thought this would generate an RID message though....). However I'm afraid this is outside my experience - my 1100 doesn't even have an O2 sensor
One thing I forgot to mention above is that bad valve clearances can produce these symptoms too - but I'd have thought your dealer would have checked / adjusted these during normal service or your initial fault investigation? TB sync is also pointless without checking / adjusting valve clearances first. It's easy to check these yourself if you're so inclined.
My gut feeling would still be that it's a coil / TB sync issue.
I would think it very unlikely that the symptoms you are experiencing (rough idle and high rpm vibes) will lead to permanent damage - a failing coil will probably get worse and you'll want to stop riding the bike long before anything suffers and TB sync issues will just irritate you without damaging anything.
But, bear in mind I'm guessing and it's your expensive bike
