Vibration/Knocking from primary area

You might consider closely examining the primary chain itself, there might be some rollers broken or missing. As Kommando says, run it with the alternator removed see what transpires

Once you have determined that the engine isn't rocking around and touching things, check the primary chain for lost rollers. If that is good you'll just have to keep digging. I had the same thing on a customers bike and it turned out to be a knackered main bearing on the timing side! Listening to it, you would have sworn it was in the primary case.

milfordite said:

Once you have determined that the engine isn't rocking around and touching things, check the primary chain for lost rollers. If that is good you'll just have to keep digging. I had the same thing on a customers bike and it turned out to be a knackered main bearing on the timing side! Listening to it, you would have sworn it was in the primary case.

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Yup. That's why I questioned oil pressure, a knocking rod bearing can telegraph elsewhere.

Left header pipe banging on the underside rear of primary case. Seen it before.

theocean said:

... once i pull the clutch in the knock disappears. And i cant feel it going down the road but i think thats because it gets drowned out by the other sensations/vibrations.
... what was damaged by a tight primary chain and i could order the most likely damaged parts before i actually get the chance to take the transmission and clutch apart to see.

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The main shaft input bearing stops rotating, and the clutch pushrod adds a bunch of end-load to the same bearing with the clutch pulled in. My guess is this is on its way out, possibly from the overly tight primary. I assume by your initial post that you didn't take the input shaft out when replacing the layshaft bearing (just did mine; what a relief!) so the main input bearing wouldn't have been scrutinized.

milfordite said:

Once you have determined that the engine isn't rocking around and touching things, check the primary chain for lost rollers. If that is good you'll just have to keep digging. I had the same thing on a customers bike and it turned out to be a knackered main bearing on the timing side! Listening to it, you would have sworn it was in the primary case.

Click to expand...

I have a two-foot chunk of broom handle that has helped me out countless times to locate and identify noises. Holding it to my ear with a fist around the end, the other end is held to the suspected area. It's incredible the ability of the wood to transmit sounds! I'd be for trying this trick around both sides of the transmission while working the clutch lever to turn the noise on and off.

Nathan