Sounds to me like the "clunk" you hear is just the clutch engaging. As for the grinding, if it doesn't fully shift into gear then you will get a grinding. Just the same as in your car. I have had that happen on all of my machines when I don't quite get it shifted all the way in. Very seldom has this happened to me. If it is a common issue for you then it sounds like and adjustment problem. Never tried to make any adjustments to my shift linkage before. If I remember right where the shift rod connects to the linkage on the trans. it was a flat plate with 3-4? holes in it that you could move the shift rod to. Like I said, never tried before but maybe something worth trying???