My recommendation would be just the opposite of Doug's. I agree with the statement that if you can see some there might be a lot more. Which is why I recommend doing that first.
If the rot is limited to the floorboards then it isn't too big of a job. If the floorboards are rotten then I would be concerned about the seat frames. It is also possible that the stringers are rotten, which is a much bigger task (and much more important that it be fixed before something really bad happens).
There is also a possibility that once you start really looking into the problem that it gets to be a lot more extensive than you had expected. I would not invest in a tower unless you were sure that the boat was sound.