Well if you don't have internal counterweights, and none of the nuts are missing from the big end bearing cap, I don't see that nut being loose in the crankcase causing any vibration issues. The idler spindle pushes thru the idler gear from the inside with it's nut outside the case. All the governor and cams I have seen are all pinned. The only other nuts I see on any diagram are from that vent and splash shield affair on the main case door, or from a lower splash shield with a slot in it that the dipper swings down thru. This was an original lister thing, and I havn't seen one on any listeroid. But that dosn't mean the bolt for it isn't there. It appears to be held in place by a bolt on the bottom of the smaller case door opposite the main door.
SO is your vibration really a vibration? Loose bolt between engine and frame and frame and foundation, or perhaps a cracked frame? These would allow the massive torque pulse to move the engine looking and feeling like something out of balance... Are the flywheels tight? A loose gib key will make some added noise and movement... A quick test for this is to wedge a block under one flywheel then try to rotate the other flywheel. Obviously, if one will rotate while the other is fixed/wedged, a gib key has come loose...