I put some photos in my garage on here. The bolt is a 10 mm with a washer. You'll see a picture inside the crankcase with a yellow arrow. That is the only place I can see where a bolt "might" go but it's behind the gear linkage. Hope this helps.

 

Please see the photos I added in my garage on this site. Note the one picture with the yellow arrow. It's the only place I've seen that could maybe use a bolt.

 

Afraid I can't make out what the hole with the arrow is for. Try one of the on-line parts drawings such as http://www.hondapartshouse.com/oempa...onda_atv/parts
That thick washer is for a special job, one is shown on the cam chain tensioner pivot but it looks like it goes between the tensioner and case on the drawing.

 

oil pump is what i see with arrow pointing at but the bolt you are showing is an creat bolt someone may have drop in engine.The best i rember bout oil pump mount bolts are little long then the bolt you are showing

 

The arrow is pointing to a hole behind the gear linkage. I would have to take clutch apart then gear linkage to see if that hole is even the same thread size as the bolt. But I agree. It doesn't look like a used bolt. Maybe the previous owner did some work and left that bolt in there by accident. At least I hope so because the clutch is good from what I can tell

 

Take a look at the exploded views of the gearchange and camshaft mechanisms in the parts books. There is a pivot bolt for a gearchange pawl on the drawings. Also check all bolts in the camshaft mechanism, one behind the sprocket, two for the spring loaded tensioner and one is the pivot of the tensioner/guide.

 

@merryman...All parts have bolts in them. There is just the one hold behind the gears but even that looks too big for a 10mm bolt. I don't want to take the clutch off and then the gear linkage if i don't have to.