The paint can rattle "may" be the lower timing chain sproclet. Have the competent dealer check your timing chain tension and see if this improves or at least changes the rattle, that may be a clue as to what I said about the lower sprocket. I haven't heard this rattle myself but others have talked about it and that is one cause of the noise that some dealers have found. Believe it or not... some Rockets display a valve train noise that has gone away as if it fixed itself... that also sounds a little like a rattle. I rode a demo bike that had this noise.
The runnability issue and bad idle... WilburT found that he had a bad primary throttle position potentiometer. This caused an off idle glitch which doesn't sound like your exact problem but you never know. Some people have had the entire throttle body assembly replaced which cured the problem you describe... but you know what? I'll bet that new assembly contained a new primary throttle position potentiometer...
I have yet another idea on this but I need to do some homework and diagnostic work first and with Rockets Across America this weekend it won't happen for a bit. It would be nice if someone local had a bike displaying this problem... well not nice for them but it would give me a guinea pig...
Just run these ideas past your dealer... he may have better ideas than me...