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I saw that part in the manual but when the right intake valve was at TDC, the left intake valve was also up high at the same time. After setting the right intake valve, I continued to turn the crank shaft 1 more turn as the manual indicates, the left intake valve dropped down. I was expecting it to come up a little higher. What am I missing here? Is it correct to set the left intake valve when it is on its way back down?

Okay, I'm pretty sure I did it wrong. Here is a thread on another site where some dude in a similar position is having trouble like me. I will do exactly the manual says and let you know if it works. Here is the other website's thread (if anyone is interested).
www.kawasakimotorcycle.org/forum/vintage...stment-question.html