if it took a long time to get the level of water you are describing the water must be entering at a fairly slow clip?
Anyway, I asked folks on this site previously how long it would take me to change a scupper in my driveway, a few hours was the response, so not a terrible job.
As far as suggestions for you, I can tell you what the mechanics did with my boat. One of my motors died because of flooding so my situation will most likely be worse.
Here is my thread
https://jetboaters.net/threads/my-boat-flooded-help.28858/
I don't know the exact steps the mechanics took (did they remove the plugs and turn the motor over to see water push out? did they just change the oil without messing around? I am not sure, but here is what was on the bill.
1. changed the oil twice in the motor that stopped due to water, once in the other motor. I am sure they saw water in the oil after 1 change and had to do it again.
2. changed both air filters
3. replaced the scupper with an OEM version although folks on this site have mentioned getting a 3rd party mental scupper. I might have them do that after a year or two just for piece of mind
4. I don't think they changed the spark plugs. this was my first boating of the year and the plugs were actually brand new. Maybe they made sure they were dry and left them alone?
the above bill was around $1000.00, luckily I am under warranty (until Jan 2021), So Yamaha covered that. I also had my mechanic install a high water alarm in the engine compartment. There is a small display unit with an audible alarm that is placed at the helm. They estimated a few hours @ $100 an hour, so total install under $400. I know its probably a pretty easy install, but I just wanted it done quickly.