I would check the coil for failing when hot, the control box for the ignition
system, and a loose wiring connection in the ignition system.

1994 Mercruiser 5.7 L Thunderbolt (Quadrajunk) SN 0f067387 Alpha 1 Gen 2
w/279 hours...New plugs, wires, rotor and cap @ 269 hours.
Boat would run fine at all speeds most of the time BUT sometimes after
coming off a WOT run engine would not run below 1200 rpm. Stumbles, etc as
if it was starved for fuel. Makes it interesting trying to dock. Had to baby
Mercotrol to get it to stay running at that speed. Any speed above that runs
fine.
First time it happened I suspected bad fuel (boat had set for sometime with
1/4 tank). Added 6 cans of B12 (50 gal tank) 6 cans dry gas, sprayed carb
down with carb cleaner (lots of gunk) and changed the Merc fuel filter water
separator. Opened primary mixture screws to 2 turns (was @ 1 1/2)and all
seemed better.
Boat ran fine for next 5 hours, but did have a wandering idle and has always
been hard to start from cold.
Now, on last trip, same thing happened again.
Drug it home,put muffs on, fires right up. No problem.
Let it warm up and try to restart. No start.
Check fuel- yep, accel pump squirts it out. Check for 12v at both sides of
coil. Got that. Pull distributor cap and check rotor and inside of
cap...looks like new. No spark though, verified with timing light.
Check for loose wires, blown fuses, etc...none found.
Now....do you think the 2 events are related?
I would think that if the Thunderbolt went south it would be an all or
nothing event, not a random loss of low speed.
Ideas, men, ideas.

--
"Only the dead have seen the end of war" Plato