[Kahuna]

Hi Tub
How was the clearance checked?
Was a compressed gasket used?
Were the measurements taken with the compressed gasket thickness or no gasket?
Essentially you want around .045" above pistons with the gasket installed. No more than .050". Some go as low as .035".
As you mentioned, it's a great idea to equalize the clearances on both sides of the engine with the gasket installed.
This will give you the best economy & performance.
Jim