Maui
As Dave said, you have to know where to check for PTV clearance. When the cams are in the overlap position, That is at the top of the exhaust stroke, when both the intsake and exhaust valves are open at the same time. Ehhaust almost closed and the intake just starting to open. that is when the valves are the closes they will be to the pistons.
The clay method is fine if you have the engine apart, but if you put a mild cam in an assembled motor and want to check it for PTV, you can put in into the overlap phase, put an indicator on the bucket, zero it out, and push the bucket on down until you feel the valve touch the piston. Take a direct reading from the indicator.
I have not had the chance to do this on a 'busa yet, so I don't know how much room there is to get on the bucket with the cam lobe in the way. On the older GSXRs and GS motors with rocker arms, this is by far the easiest way to check the clearance.
Jay