Yes like daman says, read the tech pages and search.
I am afraid you guys may be making this more complicated than it needs to be.
The valve simply adjusts the port height (the timing of when exhasut gases can escape from the cylinder). It is the vertical height that matters the most.
The pic that S.S. Viper posted is in the closed position like he suggests. He likely did this so you could see the valve. His advice is good too, you want the leading edge of the valve to be flush with the passage when the servo is at full open. Using the starter (choke) flipper is the easiest way to get it to idle down to 900. Marking the pulley like suggested is a good idea.
Someone else mentioned feeling for a thin piece that moves to find the valve. This is very easy once you have done it a couple times. In fact if you push the valve up it will only go so far and stop. This is the Yamaha adjusting measurement in the manual. Remember you want to adjust the leading edge (towards the cylinder) to flush at full open. The valve end is machined so that both edges will likely be flush, but the leading edge is the important one.
The Yamaha method does allow for stretched cables. What you are really measuring at the housing is how much free play there is at the full open position. The valve will actually travel on into the housing a certain distance before bottoming out. This is method is not as accurate as the "feel" method, but it is close enough for those who are not looking for optimum results.
Yes, there is a stop machined in the cylinder that the 2 tips of the exhaust valve will rest on if it is allowed to drop freely. However, if run long enough the softer valve material can peen over and contact with the piston can occur. I have seen several like this, but all of them were run quite a while with a pulled through or broken cable.
Not trying to insult anybody, just trying to help. These valve are very easy to adjust really.