Sounds like you've narrowed the problem down to the final shaft bearing, oil guide, sprocket or chain. Probably chain or sprocket loosening up.
FYI...
When the engine is running (Engine is driving)
With the clutch engaged: crankshaft is driving the mainshaft,
...and in neutral: the mainshaft is not driving the counter shaft.
...and in gear: the mainshaft is driving the counter shaft and final shaft
With the clutch disengaged: crank is not driving the mainshaft,
...and in neutral: the mainshaft is not driving the counter shaft,
...and in gear: the mainshaft is driving the counterhsft and final shaft
When engine is not running (Rear Wheel is driving)
Chain is driving the final shaft, final shaft is driving the counter shaft
And in neutral: coutershaft is not driving the mainshaft
...with clutch engaged: mainshaft is driving crankshaft (not moving)
...with clutch disengaged: mainshaft is not driving crankshaft
And in gear: countershaft is driving the mainshaft
...with clutch engaged: mainshaft is driving crankshaft
...with clutch disengaged: mainshaft is not driving crankshaft