You can find fish and shell fossils in the moutains. How did they get there? They must have been covered by the ocean. How did the land animal survive if the land was covered with water? They must have been saved in a boat. You'd need two of every animal (basic reproduction). Noah and family would need 7 clean animals so they could have something kosher to eat during their trip. How did the flood happen? A whole lot of water from God. Why would God flood the land? There must have been something really awful that he wanted to wipe away.
The whole story is easily created by looking at the world through ancient eyes and asking, "Why?" You don't need a real live historical flood to get this story. And, no, I don't think the inclusion of something fictional means that the whole Bible is fiction. I would be surprised if some Ancient Near Eastern mythology didn't make it into the Bible by accident.
Well, I sppose so. Of course, people have cited the same facts as you - sea shells on mountain tops - as evidence for the Flood. But I rather doubt that's how the story got started in the first place. It seems more likely that the source of a flood myth is, well, a flood.
Recall that the myth originated in Sumer, which doesn't have much in the way of mountains, but which is pretty flood prone country. All it would take is heavy rain, an unusual amount of water in the rivers, and maybe strong winds backing up the water in the Gulf.
The "sea breaking in" scenario has also been around for a long time; it was popularised about 30 years ago in a novel by an author whose name I forget, but he had the entire Mediterranean basin flooding.
The Black Sea hypothesis is interesting but, as the article points out, it simply wouldn't work. There is a net flow of water out of the Black Sea, and there has been for a s long as the Russian and Balkan rivers have been there, which is a long time. So closing the Bosphorus would cause the water level in the Black Sea to rise, not fall.