Yes I feel badly for her. And, she knows her boat to a point.I'm just shaking my head when I hear stories like this. Fortunately the owner has a great friend who can fix anything ready to help her.
Reading your list......
It would appear that the work and early performance issues were related to the plug wires crossed. Rookie error by the "mechanic" and who in the world replaces a cap without replacing the rotor?
The problem you are chasing now appears to be the carb running out of gas. My money is on the float level of the carb. The fluid tests indicate that the pump is performing and while air could be getting in......I just have a feeling the float is the issue.
In regards to the fuel pressure set up.......There usually is a spare port on the spin on fuel filter mounting that is on the pressure side. It is an easy way to tap the line if it has one.
There isn't a filter that I know of downstream of the pump other than the screen in the carb. Only the filter/water separator on the suction side. I gotta tell that I've only built a thousand carbs but as Regan said "trust but verify".