Check your flywheel mark just once to find TDC for either cylinder. Mark the cylinder number and location at the exact top your crank sheave. The photo below shows my engine at ANY LOCATION. It is not being checked for lash.
The other cylinder will be at exactly 180deg. from the first mark. Mark that one as well.
When you want to check the lash on #1 cylinder, place the #1 mark at the top and make sure the rocker arm doesn't move when the engine is slightly turned. If it does, rotate the engine 180 deg.
Below is an extract from a Seloc manual which, in this case, might be a little clearer than the Yanmar shop manual.
Page 3-40 (below) is the start for a 2GM