I think you misunderstood about the reference to vegetation mats. They would have been huge, but not a primary source of food for the Ark animals. They would have, however, been the haven needed by insects, amphibians and a number of plant species.
If you recall, Noah only had two of most kinds on the Ark and seven, either individuals or pairs (the Bible does not clarify here) of the clean animals. Now, the only animals, in my opinion, that would have actively been breeding during that year would have been the rodents. They seem to breed anywhere, anytime, eh?
So coming off the Ark, we don't have more than a few thousand animals, a number of which flew away. We know the grass was already growing the young trees and such starting to sprout, at the least. That would have been enough for the herbivores, and the multitude of rodents would have been the beginning food for the new omnivores and big cats. In addition, there is no reason to think Noah had 'just enough' food for them through the year and none left over. The possible scarcity of ample food for a now expanding population of animals would easily have caused them to spread out somewhat rapidly.
I would like to mention that speciation has been shown to be extremely rapid when there are empty ecological niches and small populations -- both of which were in ample supply after the Flood!
About the trees underwater. Even if they could survive five months plus without sunlight or oxygen (which they can't), the sediment that covered them would have been much too extensive to permit life continuing.
In addition, if you check Genesis 7:11, you will find that the first event in the Flood was not the rain, but the bursting of the sub-crustal waters. All at once. This means that they were under enormous pressure that had suddenly reached a critical point. That kind of pressure means heat. Lots of it. Think Old Faithful magified exponentially and multiplied times thousands. This explosion of scalding waters would not only have torn up the crust around each area that burst forth, but the combination of heat and force would not have allowed anything to be fossilized.
You are right about the stomatolites. Their existence in the fossil record at the precambrian/cambrian boundary indicates a cessation of the castastrophe, and that is one reason placing the Flood boundary there makes sense.
In the geologic recored, there are four major eras, separated by three catastrophic indications. All over the world. Archaeozoic, paleozoic, mesozoic, and cenozoic eras never change places. Each has its own rock types associated with it, as well as its own fossil forms. Interestingly, the Bible also lists four major eras separated by three major catastrophes: the Deluge, Babel, and the days of Peleg.
It seems to fit. You may be interested in this:
http://www.setterfield.org/timeline.htm
And thank you for your compliments. I can see you have thought out a lot of your position, too.