The only actual criticisms of Barry's work which are not simply ranting and raving have to do with his treatment of the data (statistics). What is interesting is that this was already answered about 15 years ago in two published articles by Lambert Dolphin, physicist and A. Montgomery, statistician. Neither of these articles has ever been refuted!
In the meantime, Barry has another article in peer review right now for publishing which effectively put forward the information and some conclusions from the last five or six years of research. We are waiting to hear the reports any time (I am his wife).
About the fossils -- yes, they are less than six thousand years old, but they are not from Noah's Flood (which was, yes, a world-wide flood). The Flood destroyed so completely and fiercely that it could not and did not fossilize anything. The fossils were the results of geologic activity (mudslides from earthquakes, etc.) in the regions which maintained ongoing geological activity after the Flood. The upwelling mineralized waters in these regions (which were primarily along continental boundaries of their times and in river valleys) along with the rapid burial and draining involved are the only processes which could have resulted in these mineralizations. Keep in mind that other types of fossils can be formed other ways. Mineral encrustation does not require burial and imprint fossils are very simply made (we used to demonstrate this kind of fossil using jello!). Full mineralization (replacement of the organic material with minerals) requires rather specialized conditions, though.
The reason we see different fossils at different layers is because what was buried reflected the ecosystem that was living in that environment at the time of the burial. It has NOTHING to do with the idea that one sort of organism was changing into another sort of organism.
Hope that helps a little for anyone reading this material.