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Different part numbers, different fuel pump and injectors. PSI output from the pump depends upon the pressure regulator, not the pump.

No choke in a 2003 Yamaha F50.

What is the motor doing or not doing?

All of the Yamaha specifications can be found in the applicable service manual. https://www.yamahapubs.com/home/search?category_id=4&year=2003&family_name=F50TLRB

Posted below is what Yamaha has to say. That is all I have ever heard from them about this problem. Again, they offer no theory of operation as to what should be happening and when, and what happens if and when things don't go according to Hoyle. Millions of things in life that I have to accept...

I am thinking that I would disconnect the CDI connector and inspect the terminals, particularly those for the yellow wire. Maybe then get a 12 volt incandescent bulb that has a current flow of about 5 amps when powered by a battery. Connect the bulb to the yellow wire on the engine harness side...

When doing the compression test, was the motor fully warmed up, throttle wide open, battery fully charged and the gauge known to be accurate?

Good question. Wish I knew but Yamaha is very vague as to the theory of operation with respect to their systems. My guess is that it is to power the five volt circuit for the three wire trim sensor and other components that utilize five volts.

Did you post your problem on another forum? Sounds very familiar.

The stator has different functions. Coils to charge capacitors in the CDI unit, coils to fire the ignition coils/spark plugs and coils to charge a battery. The coils for ignition can be working just fine (motor operates normally) while the coils that charge the battery are not. Or both coils...

Weird only to those that do not yet know. What you are seeing is indicative of low voltage to the CDI unit.

It is not a solenoid. It is merely a resistive heating device that can be powered by AC or DC. Powered by AC from the lighting coil when the motor is running or powered by DC from a battery when being tested. When cold it allows more fuel to flow helping to start a cold motor. When warm it...

OP says he sees 13.5 volts at the battery. Given enough time the battery will be fully charged.

Less voltage results in less current flow. Less current flow results in a longer time to charge the battery. Just like it takes longer to fill a 50 gallon drum at 1 gallon a minute versus 2 gallons a minute. But given enough time it will fully charge the battery.

As far as I know the one, two, both, all type of battery switches have been make before break type for many years. Decades perhaps. You will need to find out how your system is wired. I can see a configuration where if you switch to the start battery the electronics will not be getting power...

What voltage are you seeing at the battery when the isolator is allowing charge current to reach the battery? Even with the voltage drop across the diode the voltage should be higher than the resting battery voltage, allowing the battery to be charged. It will just take longer.

Not uncommon for two 12 volt batteries to be connected in series to power a 24 volt device while one of the two batteries is used to power a 12 volt device. Not uncommon for two 12 volt batteries to be connected in parallel via a battery switch, or a Combiner/ACR/VAS/Isolator, so that both can...

Have you not had a boat with two or more batteries?

Easily tested using the ohm meter setting on your multimeter.