Haven't read the whole thread, but this one struck me. The Coelacanthid fishes that live today are in the same family, or perhaps even genera as their fossil counterparts, but they are NOT the same species.
Sharks that swam around millions of years ago are often not the same species that swim around today, eventhough they might be related.
Or as an example with birds: A common Chaffinch is closely related to the Brambling, but they are not the same species. Same counts for their ancestors. They look alike, but there are plenty differences as well. Same thing with Coelacanths. The ones that swam around millions of years ago, are not the same species as those that still roam the oceans today.