I read your post a couple of days ago and have pondered over the problem that you are experiencing.
In my opinion they are more than likley unrelated

, but I could be wrong. Let's start with the basics.
First question for you is... Have you made sure that all debri has been cleared from the pump housing. Just simply pulling what is sticking out won't do. Ensure that the entire pump assembly has been cleaned out.
Second is, was there water comming out of the pisser after you ran over the reed. If you got some debri into the cooling line then that would slow or stop the cooling water to the engine possibly causing an overheat.
There is no float bowl on these marine carbs so your sitting and refilling theory is out the window.
These are the next basic questions that I have asked myself if I was there looking at your ski.
Is there enough fuel in the tank, are you in the on, or reserve position on the fuel selector. Have you been maintaining the 2-stroke oil level in the oil tank.
Let me know the results of these questions and then we will work from there.