I don't know if I would say that "earlier models have a high % of engine bearing failures and transmission problems". Remember that we rarely hear about all the happy owners who have had no problems. It is only human nature to speak up when things go wrong and to stay quiet while everything is fine.
That said, I did own a 2005 RIII purchased in mid-2004. After 42000 miles the shifter linkage inside the engine came uncoupled leaving it stuck in 5th gear. Triumph agreed to fix the problem and also install the upgrade kit which effectively brought the entire bike up to 2007 model specs. My only expense was the time and gas to trailer my bike to the dealer.
I no longer have my RIII but would not hesitate to buy another bike from Triumph knwoing how well they stand behind their products.