I like it. You could try first "building" a realistic floating zoo, and noting that things were a bit cramped and unsanitary you would note that "obviously", during the ark time animals neither ate nor excreted. When the ark still didn't fit all the animals, you could note that "obviously" the animals were shrunk to miniature size.
Or maybe, you could put forth different theories on how to make the ark "work". If you could figure out how big a realistic ark would have to be, you could use that measure to determine the size of a Biblical cubit. 18 inches is often used as a standard cubit measure, but it's actually the length from the elbow to the fingertips. Now, consider for a moment that just before the ark story, Genesis 6 talks about the giants in the Earth. Obviously, once you calculate the size the ark would have to be, you could use that to determine the size of a cubit, and it would "prove" that there were, in fact, giants in the Earth, and you could use the cubit calculation to determine the size of the giants, because obviously, Genesis was using the "giant cubit", based on the size of the giant's forearm.
I think this has real potential.