If you have the clip under the kill switch, do you have the key out of the off position? Both do the same thing, ground the CDI to keep it from firing. Fixing one without fixing the other will make no difference, their purpose is to turn off the engine.
You have to give more information as to what you are doing or we can't tell you what to do differently.
If you replace the ignition switch rather than having a locksmith re-key it, you can get one that has a safety switch built in. You push in on the key and attach the safety cord clip. If you pull on the safety cord it lets the key socket pop out and kills the engine.
You would already know if the floor was rotted if you've pulled the carpet up. If it's solid that will save you a bunch of time and money.
Do you hear water in the pontoons when you move the boat around and stop it suddenly? It sounds like your pontoons are made in sections that are separate from each other rather than open all the way through. Unless you hear water in them you won't have to mess with the top plugs.
I agree, put your motor problems on the motor forum rather than the pontoon forum. There's some folks there that are real helpful but they may not watch the pontoon section.
