Compliments on a detailed description of symptoms, so detailed in fact that what's not there may be informative too. I think there might be a combination of problems.
Coolant loss
The first thing I'd do is pressure test the manifold. This can be done with the manifold on the engine and is pretty straightforward. The test will eliminate or confirm the manifold as the cause of the coolant loss and point you in a direction for repair.
Original stalling problem
It sounds like it may have been fuel related as you and the mechanic suspected. The addition of a fuel filter and hose replacement probably resolved any fuel contamination problems from then on but here's one of those things you didn't say. I didn't see where the carburetor was cleaned and rebuilt. If you've owned the boat for 6 years, had possible contamination problems and haven't rebuilt the carburetor, it's overdue. It should have been done when the filter was added for a complete repair. Even if the carburetor is clean, where's the harm?
Electronic ignition upgrade
We're all thinking the same thing. Let me ask this specific question though: you correlate the current stalling problem to engine temperature but can you instead tell us the time line in a stalling episode? What we're looking for is somewhere around 45 minutes run time before the engine slows and dies much like fuel starvation. Following a 20 minute or so cooling off period she'll start only to stall again after a little less run time.
Here's my guess of what's gone on:- 24 year old installation with a deteriorating fuel system. Possible hose decomposition due to ethanol in non-ethanol rated hoses and possible tank contamination. Issue resolved with hose replacement and filter addition.
- Electronic ignition upgrade performed at the same time as the fuel system repairs which brought on another problem with similar symptoms as the previously resolved fuel issue. You traded one problem for another. I did not read the coil was replaced in the EI upgrade. This is critical with electronic ignition.
- I don't think the coolant loss is contributing to the stalling problems.