How can the Flood explain biogeography ? According to the Flood story all the surviivng animals ended up at a single location. How they spread out from there is the issue and there is no reason to suppose that that would have anything to do with the biological relationships.
Want to explain why Australia had, for instance, "marsupial wolves" rather than wolves ?
You need to do more research on polystrate fossils. They were explained in the 19th Century. This article refers to that explanation
http://www.talkorigins.org/faqs/polystrate/trees.html
By your comparison it seems that you think DNA is a simple structural material with very little variation. That is not true - the primary function of DNA is not structural, the sequence of the constituent units codes for the protiens which are used to make up the organism. It is not just a repetitive structure of identical elements as our analogy suggests.
The number of chromosomes has very little to do with complexity. Especially in plants where the entire genome is quite often duplicated in reproduction (polyploidy). And you have to remember that modern ferns will be different genetically from their ancient ancestors.