Evidence is pointing more to the transmission. There was no need to pull in the clutch while rotating the wheel in neutral - the input shaft is disconnected from the power train at that point. But the output shaft IS still rotating, and that's the one with the troublesome bearing.
The front (towards the front of the bike) bearing on the output shaft is the one that normally goes bad first. What tends to happen is the bearing cage fractures, and since that bearing is somewhat isolated, the debris recycles through that bearing. Once it starts to go bad, it disintigrates very quickly. But the first thing to go is the bearing cage. Without the cage to hold the large ball bearings in place they migrate to one side allowing the shaft to shift, which then minimizes gear mesh. That clunk you're feeling is the shaft flopping around in there.
Checking the magnetic drain plug is easier than separating the driveline, so I'd have done that first. If concerned about possibly unnecessarily draining the gear lube, it's possible to quickly plug the hole with a finger while inspecting.
Even so, draining the fluid into a clean container enables you to easily pour the contents back in should there be no contaminants.
What you're going to find on the magnet is more than soft fuzz (acceptable) - it's going to be slivers and chunks.
This may seem like horrible news, but there is an up side. You're extremely fortunate to discover this now rather than on the next ride when the box starts emitting screechy clunky noises and the gears are trashed and not re-useable.
Since this is a new bike to you, I'd contact the seller and let him know what you've discovered. Hopefully he'll refund some of the purchase price. So hurry up and check the oil - that's an important step in diagnosing this one.
