Not all the water came from rain. Scripture describes God "as opening the fountains of the deep". There were probably geological changes of significant magnitude going on. We know that it rained on Noah for 40 days and nights.
The PDF file addressed the "boiling of the seas" theory. Explaining that's only true if the energy is evenly distributed which it wouldn't be.
Since you don't know what the geography was like before the flood, you really don't know how much energy it would take to flood the earth. Nor do you know how the earth would react and handle that much energy.
Re: the global flood. See #634.