I recently had a starting issue with my 90 murray - checked for spark, had it - gas was there, would just refuse to start. I touched the mag wire end to get a nice solid jolt while cranking - baffeled me on its issue.
Checked air gap on mag, cleaned flywheel, mag ends, checked flywheel key, unhooked the mag kill wire - so as a last resort i dug out a good spare mag i had , bolted it down and cranked it up- fired right off.
Ive had a few of my tractors intentionally down in the swamp behind the folks house back north , water splashing everywhere - water as deep as the bottom of the carb - they always brot me out.
Id say to see if it still runs, isolate the motor and ignore rest of ign system( for now) - unhook the mag kill wire and stator wires and try starting the tractor directly with leads on the starter motor .
It should start - possibly the mag was hot, when it hit the cold water and fried it - id pick up a new magneto reguardless.
Have you checked the flywheel key? Might not hurt to take the shrouds off and see if its still in spec- i imagine being submerged running under water couldve popped the flywheel key ( water wont compress).
If it runs with the original magneto isolated, then its else where in the electrical system is the starting problem .