You guys are funny!
Actually, once you've seen it a few times, it's a 'no brainer'.
Right now I'm working on two transmissions (with a third coming) with the same common cause for tear-down - the front output bearing. Of course, there can be other things, like the shift pawl spring, or worn bushings that allow it to pop out of gear, broken dogs - but that bearing is the biggie.
One of the trannies just needed the cover replaced due to (what appeared to be) a broken output boot flange from an accident. Once opened, there was shinny sparkly gritty stuff sprinkled around. Bad sign. Turns out the output front bearing had slid on the shaft (no circlip) and was beginning to deteriorate - sloppy. That's where the debris was coming from. Luckily it wasn't very far along and the rest of the transmission wasn't harmed.
Maybe five years ago my R80G/S started making whining noises. I noticed the oil was sparkly and the magnetic drain plug had slivers on it. Right then, if I was smarter, I'd have known to retire that transmission and get it worked on. But I wasn't, and I didn't, and added some Lucas oil additive hoping to quite things down and... who knows what I was thinking?
So I rode it another thousand miles like that and it seemed to be fine. Until...
I was 400 miles from home heading to Crescent City CA (about 20 miles away) and got horrible crunching noises in the gearbox. Nothing I could do at that point but stay out of third and fifth. Rode it another couple hundred miles that day to a friend's place, and from there trailered it home.
That was one of the first transmissions I worked on, and let me tell you, it was sickening - trashed the fifth gears and made a mess of a lot of stuff. All because of the front output shaft bearing!
So you don't need to ask me, because you now know - I've been there, done that, got the T. Personally, and seen it with others enough times to know it's very common.
Moral of the story - nip it in the bud! Recognize the signs and pay attention - if there's anything more than soft fuzz on the drain magnet - get it fixed NOW! It's a hundred bucks in parts - gaskets, bearings, seals - for a normal rebuild, but your transmission may not be worth rebuilding if taken to the extreme that mine was.
Just so you can visualize what's happening here - look at it like this:
That front bearing is a ball bearing. It's got maybe seven big balls with a cage that holds them separate from each other. The cage is two metal strips, one to a side, that are riveted between each ball. What seems to happen is the shocks and stresses wear that cage, eventually cracking it. From there it begins to fall apart allowing the balls to collect on one side - the side away from the other gear. The debris from the cage wears the bearing even more and everything goes down hill very quickly.
The clunk you were hearing or feeling was due to the bunching of the balls and the uneven rotation of the output shaft, and the uneven mesh of the gears.
