I called the dealer today and explained the situation with the Rocket to him, he said that if I checked all of those things I did, he doesn't know what else to tell except that he would be doing the same things, tearing things apart and looking. I mentioned about the thought of the output shaft bearing going bad and he did agree that could be the problem. He also said that when I pull in on the clutch lever and the noise stops that it sounds like it's in the drive/transmission part of the motor. I asked about bringing the bike up and he said he really didn't want to see the bike right now that this is their high/busy time of year but if I wanted to bring the engine up and drop it off they may find some time to look at it.
Needless to say I'm really not impressed with the customer service from dealer or triumph rep Peter on this situation. It's like sell the bike, once it's out of warranty it's your baby, or the great phrase " IT'S THE NATURE OF THE BEAST" what bull**** !!!
If I wanted to pay for a motorcycle to set in the garage and not be able to ride it I would nave bought a basket case. you know I ride my motorcycle and it's like therapy, I call it "Rocket therapy" but I guess I'm in the "character building" stage now huh?