I am not aware of any output shaft bearings that failed twice. There were a lot of output shaft bearings on some early bikes, maybe all '04-'05? Those were attributed to the bearing being installed backward at the factory with a seal facing the oil supply and thereby blocking it. Most of those bikes failed very fast, I think in under 6,000 miles. (this is all my recollection from posts here and folks I have talked to, you will need several grains of salt for this..)
There was also an issue with a seal on the very first bikes and the entire shaft drive unit, (manufactured in Italy by a sub-contractor) was replaced on the affected bikes.
The so called "upgrade" refers to the second gear and the second gear synchro/dogs. If the gear fails, the gear and synchro are both replaced. I understand the dogs are smaller/weaker but mesh easier. When it is being replaced a few other parts are also changed, hence the "upgrade kit", but it is not an actual package, and I think the official word from Triumph is, "What kit?" That's OK by me, as it seems, with a good dealer they stand behind the bikes and most everyone gets things fixed with only a little hassle.
Still, it is a torquey motor and it seems capable of tearing up more than just the asphalt.