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Congradulations on getting th bike going, Nuke. As for the dip stick, do not screw it in to check it. If I had both, I would ditch the stick's rod and just use the site glass. You said it has been bent so I would remove it for fear of it messing with something in there.
The neutral thing? I, for one, do not put in neutral at a light. I want to be able to move right away when the light changes or, more importantly, if I see trouble coming my way. If you want to get it in neutral, however, here's what works for me. Put it in 1st, slowly release the clutch until you feel it grab, pull back in the clutch and you should be able to shift it in neutral. But like I said, it's better to be in gear and ready to go if needed. You'll have to shift into 1st anyway and it won't hurt anything holding the clutch in.
As for the clunk, it way be the revs are too high when you are shifting. Check your engine speed at idle. You may have to adjust it down, Also, a different oil may help with smoother shift. Are you using oil made for motorcycles?
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