Follow-up for someone that has similar issues in the future:
Removing & opening the FSM is easy if you take your time. Label or make a note of all the hoses. Before pics are good to have.
You don't need to remove the water hoses (starboard side) unless the case needs to be replaced.
I connected a Mighty Vac to the pressure regulator nipple before opening the box, and it held at 5psi so the little pressure hose inside that can split, was fine. My 90hp is a 2013 and it had the newer hard hose and the newer red wire FSM float switch.
I connected a Mighty Vac to the end of the vent tube pulled off of back of air filter. It held a couple psi, so the valve was closed (good) and not stuck open.
No debris or water in the fuel inside the FSM.
The FSM float switch has continuity (closed) when it's down (low fuel). The switch opens when it's all the way up. There's a switch bounce (close,very short open,close) when it lowers, but this probably doesn't matter to the software, because a new switch I had on hand does the same thing.
The vent hose end that dumps into the air filter looked clean like fuel had never gotten up that far.
In summary, I didn't find anything wrong in the FSM. I changed the low pressure fuel filter, the old one was dark inside. Maybe this was the cause of the pump timeout. I replaced the internal float switch even tho the merc original seemed to be working. I didn't find any reason there'd be gas in the oil (vac reference line was not leaking, and purge value appears to never have been open when it shouldn't have been).
I cycled the power a few times to completely fill the FSM with fuel then started it. It ran for about 10 minutes and didn't throw any faults.
