I am no expert, but could it not simply be oil?
Being a wet clutch, when the clutch is in ... the oil is between the plates and if it was cold (higher viscosity) it could easily provide sufficient drag to rotate gears in the box and graaaaate and clunk into gear. It would also provide drag once in gear to try to move the bike fwd. Question: When its hot do the symptoms reduce? I would expect so.
I also noticed you are using a 20W-60. That means that when hot it is a 60 grade oil. 60 grade is on the thicker side and is defiantly more viscous than a 30 or 40 grade. This would increase any tendency to drag.
Its just a thought.