Don,
I leave it to Simon to comment on his drawing, but guess you remarks on draining the snortmast and startig is correct with a few minor things. Basicly the starting procedure is the same as for any start. As you normally shall have some water in the chamber between the outer and inner main exhaustvalve. However if you have a massive intrusion of water you might experience a filling of the exhaustmanifold with a possible filling of some cylinders as you have explained. In any start you blow through the cylinder with open indicators cocks and the engine shall turn a few revs, you don`t open the indicatorcocks to "make it easier to turn the engine", the reason is to blow out possible water in the cylinder through the open indicator cocks to prevent waterstroke. The starting airpressure of 30 kg/cm2 is ample to run the engine easy on air only, but you want to prevent water strokes, hence you want to get rid of the water in the cylinder which might created a major damage by a reciprocating engine. Only in extreme cases you crank the engine by hand, not normally, as air shall do the job easy having an experienced engineer at the starting handle bowing out the trapped water in the cylinders flooded.
I noted some place you mentioned we dived with the snortmast raised, that is a misunderstading, we normally raised the snortmast submerged but raised the mast for maintenace surfaced, see the image below, however we did we never run the engines with the mast raised on the surface as the mast did not have any cooling and the greaseingpoints could be ruined.
Tore