Does it still do the same thing when you remove the chain?
If it doesn't, try this to see if it's the transmission/engine:
-Remove spark plug
-Remove chain
-Rotate engine over in neutral by hand with kickstarter and listen for sound, if not present continue to next step
-1)Put into gear and rotate engine, check all gears, listen for sound
-2)Put into neutral, remove chain from rear sprocket to bypass axle, pull the engine over by hand with chain, listen for sound.
If you can isolate it to the engine, then you know for a fact there's something wrong with the engine/transmission.
Before you take it out and apart, check the most accessible parts of the engine first.
Remove stator cover and flywheel, make sure nothing is loose, don't forget counterbalancer.
Remove clutch cover and look for any issues.
Drain transmission oil and check for metal flakes, shards, or lots of powdered metal entrained in the oil.
The idea is to inspect and identify the problem before having to spend a lot of time removing the engine and splitting the cases...that's the last step to take.