the Directions for making the ark are in Genesis 6:15 and 6:16
6:15 And this is the fashion which thou shalt make it of: The length of the ark shall be three hundred cubits, the breadth of it fifty cubits, and the height of it thirty cubits.
6:16 A window shalt thou make to the ark, and in a cubit shalt thou finish it above; and the door of the ark shalt thou set in the side thereof; with lower, second, and third stories shalt thou make it.
A major problem with large wooden ships is that they snake and hog as you can read Here. These shape changes are unavoidable with any wave action at all and the tendency of a beam to flex increases with the cube of its length. Large wooded ships like the Wyoming required constant pumping. The ark would spring leaks all over, pitch or no pitch.
It seems to me that just about the worst thing you could do under these circumstances is put a door in the side of the boat. It just gives you an additional place for the ark to spring leaks and will really undermine the stability of that side.
You also have a boat with no steerage drifting around in global rainstorm for 40 days and nights. Enough water would come in the window to sink the ark nearly as fast as it would sink from leaking at the seams. Remember that even a mere thousand feet of global rain requires it to rain a foot an hour the entire time.