The discovery of a living coelacanth is exciting but it is in no way a challenge to TOE because it doesn't break the pattern. Everything is still in the right order. The modern coelacanth is actually not entirely identical to the fossilised specimens, but it is certainly of the same family.
The order of origin is more important for TOE than the time of extinction because TOE predicts that species can only evolve within the limitations prescribed by their immediate ancestors. TOE predicts only that many species will go extinct, and sometimes how, but not necessarily when.
As I have stressed throughout, TOE does not necessarily mean that simple forms disappear as more sophisticated creatures move in. If the simple lifeform has an environmental niche and can compete successfully, it will continue. (Possibly this is what happened with the coelacanth as it lives very deep in the ocean.)
Whereas an ape, for instance, has fewer places to hide. Of the estimated 8.7 millions species still living on this planet, only about 1.2 million have been described. However, most of those are insects and plants, it would be a big surprise to find a new large mammal.
As for the accuracy of fossil dating....specific fossils are always found in specific geological strata. eg a fossil may first appear in a layer of Devonian sandstone and never in an earlier stratum. Geologists have built up an accurate picture of the layers of rock through the ages by cross referencing samples from all over the world. Fossils are a valuable contributor to this record - and in fact they play a big role in oil industry prospecting, because they are such a reliable indicator.
Fossil evidence is cross referenced with evidence from other disciplines including geology, radiometrics and molecular clock estimations. (In fact, one of the convincing aspects of TOE is the way it supports and is supported by other sciences).