If the engine is directly coupled to the prop shaft that might be why they were coming in too fast, when they tried to slow down it stalled. Just a guess on my part but I think something went wrong with fuel delivery, may explain the black smoke as well. FWIW.
I'm guessing that it may have had a thru hull fitting at one time to feed water to a live well. If you have no need for it I would cover it permanently by replacing the plate with a solid piece of aluminum. Like you mentioned the hole is in a place where a plug could get knocked out by mistake.
I think i see daylight thru the hole and have no idea what it's for. maybe you could remove the extra metal plate and replace it with a new solid plate?
If you're comfortable with the present handling which it sounds like you are, I would leave it as is. New steering gear wouldn't effect the pull when getting on plane.
Yep, I think the same, lock the guns and ammo but leave your favorite on the nightstand. I don't have youngsters, if I did the one on the nightstand would be hidden but close..