With pistons of 1″ diameter and say valves of 1/4″ diameter there will always be a lot more area for pressure to act against on the piston than the valve. Basic lbs per Sq inch
If a 180deg crank is fitted then there will be power to one piston almost all the time so you have 8 times as much force on one piston than the two valves added together so the engine should be able to overcome any valve issues.
With the 90degree crank you are only getting power for 3/4 of each revolution at the most. The remaining 1/4 of the revolution when neither piston is on a power stroke will get the full force of the air against the spool valves and that is likely what is stalling the engine. Even if the valves are redesigned to use springs the engine has to be able to compress those springs when there is no power from the pistons.
If you look at the popular twin cylinder single acting engines like the Stuart Sirrus, Star, Sun, MTBs etc they all run 180 deg crankshafts. As there is always power to one piston to push the spent air/steam out of the other cylinder which also helps