what about the FOXP2 gene? Apparently in that skull it is so different to humans that it could not be the same creature.
He repeatedly says "the gene is 2,594 base pairs long".
Not quite, it actually has 607,463 base pairs. That alone makes it hard to take him seriously. The FOXP2 gene is also nuclear DNA, which degrades fairly quickly, so it's not exactly surprising to see variation in a 900 year old sample that's been in the possession of several families and exposed to all kinds of organic matter.
This really has nothing to do with science. Pye is looking for a specific conclusion and bending whatever evidence he can find to support it, instead of going where the evidence logically leads. He finds gaps in information and decides that supports an alien explanation, which is ridiculous. The fact that no official studies or reports have been released by a credible lab or geneticist makes it even harder to believe.