Slight knocking sound in transmission case?!

Prior to tear down of my KZ440 Ltd (belt) there was a knocking/ rattle sound coming from the transmission case. It sounded much like a large ball bearing rattling around in a tin can. The puzzling part for me is that it only makes the sound when in low speed when coming to a stop. Regardless of having the clutch in or not. It's quite loud as both my neighbour heard it as I was coming to the stop sign near our houses. I put the bike up on the centre stand in the driveway and ran it through the gears up and down to replicate it on the road but it doesn't make the noise. It seems to only do it under load while riding. Help would be much appreciated. Thank you

Does it make the noise when the engine is idling at low rpm?

I'm checking to see if the 440 uses a primary chain, as a primary chain drive can make a deep knocking / rattling sound at low rpm, especially if the carbs are out of synch.

Yep, this engine uses a primary chain (crankshaft to clutch basket) and also a chain to drive a counter balancing shaft, which is common with Japanese vertical twins. Both could be the source of the noise. Chains and guide system parts could be worn out, or carbs are out of balance (synch), causing uneven idle and excessive torsional vibrations. If the chains, chain guides, tensioners, etc. are worn out or damaged, the engine needs to be disassembled (again).

Before you do that, get the carbs synched, adjust the idle speed to the specified rpm, and see if the noise is reduced or eliminated.

Another possible cause of a noise like that is bent, incorrectly assemble, or worn transmission shift mechanism, shift drum, shift forks, etc. The sound could be the transmission gear dogs striking the gear dog slots due to improper clearances. One bike I had did that for years before I tore it down to find the problem. It sounded like a party noise maker or a giant socket ratchet wrench while coasting or decelerating in first or second gear - it was a bent 3-4 shift fork. Only the shift mechanism is serviceable without disassembling the transmission. Otherwise, you will need to disassemble the transmission to check and repair.

And don't overlook the final belt drive - check that the belt isn't hanging up on something during deceleration - make sure the belt is tensioned correctly (adjusted) and is running free while loaded in either direction. Keep in mind the belt tension is different when the bike is on it's center stand vs. when it is ridden on the road...

Good luck - hope that helps...

Awesome a full list. I certainly do appreciate your insight.
The nearby Moto shop wouldn't give me the time of day even while I was spending money with them.
Very glad I joined this group. I will keep you apprised of how I make out.

Thanks again.