Another belated response.
Two cranks at 90 degrees, will, if put into static balance, should each be in Primary balance.
The fact that the cranks are at 90 degrees, will mean that they are also in Secondary balance, although, because the cranks are not in the same longitudinal plane there will be some couple acting on the engine. This will give it a tendency to squirm around a vertical axis.
What will determine how smooth, (in terms of vibration) the engine is when running is the proportion of Reciprocating mass that is balanced as compared to Rotating mass. You can spend a long time experimenting to optimise that!
The mass of the flywheel will have no effect on vibration (unless the flywheel is out of balance!). What it will improve with increasing mass is the smoothness of angular rotation speed. Whilst a heavy flywheel will minimise the speed variation at the flywheel end, it is likely to increase the speed fluctuation at the free end (Torsional vibration) This is because the heavy flywheel tends to act as fixed point about which the flywheel can vibrate in torsion.
In a two cylinder engine, unless the scantlings of the shaft are such that the pins and journals are thin and long, it is not likely to be a problem.
If you were making a high power eight cylinder engine, with nine main bearings, it might be another story!
Lanchester Harmonic Balancers are most often applied to four cylinder engines, although the trend towards three cylinder car engines makes their use more likely. The balance shafts, with their balance weights have to be timed to the crankshaft and each other, and geared to run at twice engine speed. If the balance shafts are not accurately timed to the crankshaft, the engine could turn out to be coarser than without them!
The function is that the secondary out of balance forces from the balancer shafts oppose the secondary forces of the reciprocating and rotating masses and so, to an extent, cancel them out.
On a twin cylinder steam engine, I have never heard of their use (but there may be examples), and are probably not needed.