Wow.... rod knock in a tranny... that's new. :P
I'd start with inspecting the drive shaft and the center carrier bearing in particular. Then I'd pull the inspection plate on the bell housing to have a look inside; If it's a W58 you're only option is to loosen the bell housing all the way around and pull the dust cover. Hopefully, it's the drive shaft or a shot damper in the clutch disc.
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