Took delivery of my Ultra in September, and it ran worse than the 1995 Ultra that I traded in. Stalled, at times felt like you were taking off in 3rd gear. This spring did the SE Air Cleaner and SE Pipes, the dealer did the 25 Degree injectors and the download. Bike now performs flawlessly.
Not sure exactly which part what made it run so much better (injectors or new map/download), but I am a big advocate of getting them replaced.
I had the 8* and didn't notice many of the problems you read about, occassionally though I'd have he hard start problem. That said, I do have the SERT and I think the SERT and PCIII with a map compensate for the 8s... Anyone that responded as to not having problems, are you running only the stock ECM or an additional tuner?