For the original poster:
New TSB for 6-Spd Transmission flare
It's in the Sticky: General Gen 6 Info.
As for the question above regarding the 4 cylinder flare... You have a few options:
As your car has gone well beyond the 60K mile powertrain warranty, you will have some trouble. If you want the dealer to fix it under warranty, or without charge, you'll have to prove that the condition existed before the 60K mile warranty expired. (Multiple receipts showing that you have tried to have the dealer fix it before the warranty expired) You might be out of luck because you waited so long. (28K miles out of warranty)
That said, your options: (most likely a combination of 2,3 and 4)
1) Live with it. (probably not what you wanted to hear, but it is an option)
2) Try a different dealer.
3) Insist that the mechanic or service writer "ride along" so you can demonstrate the flare.
4) Call Toyota's Consumer complain line, or ask to speak with the dealership's service manager, or go up the chain of command until you exhaust all options.