I am having the same issue with my 2019 50 efi and just today ordered a new coolant temp sensor as I believe there is slight white smoke coming from my exhaust. I have replaced spark plugs, changed oil, thermostat, new impeller, fuel filter, high pressure pump. All this year.
Motor ran fine all last year over 100 hours logged . My problems started this Spring as there was crap in my VST and took out the pump. Took motor out for first time and got a continuous alarm while running. Guardian mode kicked in but not a big drop in power like a low oil pressure or over rev code so thought it may have likely been an overheat so did the therm and impeller. Since then the second beep is always present on startup. I use my motor for crabbing and haven't had much time to chase this until now. Actually switched out boats and started throwing parts at the motor. Finally , I ran the motor for 8 hours over the weekend and aside from the light puffs of white smoke it seemed fine. There is no water in my oil. My motor always starts immediately it is just that once started I get that 5-7 second beep it goes away and no beep or beeps all the while the motor is running all day. Annoying because I want it perfect.
I have also switched out batteries. Backflushed the motor and noticed that while on the hose no white exhaust. Going to pull the plugs and compression test this week. Running out of ideas but will go over my wiring as the current drop makes sense to me.
Curious what they charged you to do the CDS scan that just maybe my last resort, taking it to the dealer.
I also have an older 2009 60 efi that is on another boat that has been flawless.
B
Just saw you may have a solution next time I run will be watching the fuel filter bowl.. that makes sense too as my problems started this year in the fuel system but my motor starts instantly...just throw out that second beep.