Pistons are numbered 1,2,3,4 from left to right. Pistons 1 and 4 are at top dead center at the same time, so the mark on the crankcase corresopnds to TDC for both. (when 2 and 3 are at the bottom of their stroke.)
However when #1 is at the top of the compression stroke, the cam lobes are in a position (pointing up and away from the valve lifters) different from #4, which is closing the exhaust valves and about to begin the intake stroke (cam lobes are facing down, either ending or just beginning contact with the valve lifters)
Measure clearance at the cam lobes facing away from lifters.
When you're done taking the first four measurements, turn the crank 360 degrees to #4 TDC (it will now be in compression) and measure the other four listed clearances.
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