If you are having the pump replaced this week, then I wouldnt worry too much.
As far as trouble shooting goes, the facts are that you ran through some mud, lost the water stream out of your pisser, and then got an overheat alarm. If all of this happened in a short amount of time, then most likely you lost water pressure going to your powerhead. If it were just a clogged pisser, you would still have water circulating around and probably wouldnt have got the alarm so quickly. The pisser is just a bleed.
If you lose the stream, sometimes you can try giving the engine a quick rev to try to increase the pressure to clear the weeds or whatever. But if you are already overheating, you dont want to make you problem worse.
When you restarted to go back to your slip after sitting a while, did the engine Pee then?
Again, I wouldt worry if your getting work done this week anyway.