I called a local shop that has been around since the 60s that knows how to work on these bikes. He said the tensioner is probably OK, but to pull the pan and see if theres an rubber bits, etc. floating around in there. I pulled the pan and everything looked OK. Some small sludge at the bottom, but nothing extreme. I looked up there with a flashlight and didn't see anything funny, actually looks very clean in there. Gears looked good too. Primary chain has a bit of slack and some side play, but I think it's probably OK.
The shop also said that considering the amount of miles I put on it (about 6,000 in the past year) and the relatively low miles (25,000) that the Primary would have progressively worn out, and he said that pulling in the clutch will change the noise as it's starting to wear, typically anyways. So he said he was pretty doubtful it was that. I tend to agree, considering the noise is incredibly loud and clearly from the right side of the top of the bike.
I bought a proper mechanics stethoscope and the noise seems the loudest on the exhaust flange for cylinder 3. While I was at it, I checked the valve clearances and they have drifted a little bit, but nothing seemed way out of line.
At this point, I guess I have to pull the head off and see what the deal is. Not sure why I am having this issue; I was pretty good about changing oil, checking its level frequently to learn how often it needs topped off, and things of that nature.
Will keep everyone posted when I finally get around to pulling the head, as I will need to arrange having it stored somewhere in order to leave it in that state. I'm guessing I'll probably have to take it to a shop to have them check the tolerances if I see nothing obvious.