try adjusting cylinder 1 @ TDC then rotate crank 180 degrees and adjust cylinder 3 @ TDC then rotate crank 180 degrees and adjust cylinder 4 @ TDC then rotate crank 180 degrees and adjust cylinder 2 @ TDC. adjust the valve stem clearance by following the firing order.
Does this make sense ?
Also, there are two different valve stem clearances......one for adjusting while engine is hot and one when adjusting while the engine is cold.
As im sure you know..........if the clearance is not enough, the valve will not seal and you will appear to have no or reduced compression.

Also.........just giving your predicament some further thought...........if you are running twin sidedraft carbs, it may be possible that the idle circuit on the carb on cylinder 3 & 4 is blocked or not adjusted correctly.

Benny