I'm leaning toward Flood = Rain = Rani. But that's pretty much exclusively based on the name and the fact that she seems aware of Time Lord stuff (particularly the TARDIS).
But... I'm not as familiar with pre-9th Doctor lore, but my impression is that the Rani was very much a cold calculating scientist type – as in, "I'm going to run this experiment and see what happens, and while I don't want the people of this planet to die, I don't particularly care if they do." And that's not the vibe I'm getting from Mrs. Flood. And RTD's been doing a lot of stuff with names and anagrams, but I'm thinking this might be a red herring, similar to how S. Triad = TARDIS was last season. So I don't know.