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That's 9 meters of rain per square meter every hour for 40 days...

If the amount of rain were the determining factor your point would be valid.

However, the viewpoint of the YEC is that it was not so much the amount of rain (as in your thunderstorm scenario) as it were the amount of water from below which came up rapidly due to a one time geological disaster, (the biblical term for this subterranean water was 'the fountains of the deep or the great deep'...if I recall correctly).

Any YEC may correct me if I am mistating this and I do not say this is the claim of all YECs.

The lion's share of the water did not come from the thunderstorm you outline, but instead came from water previously held under great pressure from below the earth's crust (most of which is now contained within the much larger ocean basins.)

For sake of argument, given. Lets say 99% inflow and 1% rain. So that is a tsunami level turbulence while enduring a storm that is still 4 times worse than the worst thunderstorms. And lets figure the atmosphere gets a bit churned up, I mean fill a bottle with water and watch the air flow out of the top.

Moving mountains, upwelling seas, you say God can do it, and since it cannot be proven or disproven I'll ignore it for now.

The ark is a very different matter. God may have provided the blueprints, but it was built by Noah and his sons. It is a work of man, with mortal tools and materials. Wooden boats tend to hog (bend in the middle in high seas) especially if they are built to large dimensions. This opens up seams and weakens joints. Now the dimensions given in the bible seem to indicate a big barge. It is not going to maneuver well, if at all. That might do OK in calm seas, but if the water gets turbulent it is going to either break up or founder. There is a limit to how large a board can be cut and moved using manual labor. Noah didn't have modern cranes and a saw mill. He doesn't have bolts or probably even nails so this is mortise and tenon construction. Oh and no latex caulk for the seams, just pine tar and rope. And the caulking job better be good because there is no diesel generator to run the pumps.

So we are talking about a ship with millions of hand made joints and miles of caulked seams. All of which are not going to stay water tight for very long in rough water. Go watch the video Perfect Storm and keep repeating to yourself leaking wooden boat.

So you would need to take the boat the guy in Holland built, ballast it, then run it through a Hurricane every day for a month and a quarter. That still isn't a valid trial, as the turbulence in the biblical storm would actually be much worse, and the rain slightly heavier.