I had a friends boat roll down hill and his trailer hit my boat hard enough to put a crease in the aluminum, I filled the boat with water to make sure it didn't leak anywhere around the damage, it didn't so I called it good.
Your problem sounds like a damn nightmare, I would just leave it alone. Unless you are getting a ton of water in the boat, who cares if there is a couple gallons under the floor. I always pull my plug on the ramp to drain water that might be in the boat out, sometimes not one drop comes out, other times seems like there is 15 gallons pouring out. Not sure why one time its dry and the next not?
I sure am not going to remove my floor, wow for a ton of work for a bit of water.
Good luck I hope you find it.