Perhaps the answer to the species problem will be a way of describing a species by the relative nature of its genome
We have 3 billion basepairs. About 32 million basepairs code for proteins - that leaves 98% that doesn't. Other molecules such as miRNA's and siRNA's are being discovered that have a huge impact on the expression or suppression of other genes. Some of these are even encoded in endogenous-retroviruses that infected our ancestors.
The genome is not anything like a blueprint - that is a terrible analogy. It is perhaps more like a recipe where small changes in ingredients or methods can have big effects on the results. A change of a single letter in a genome of 3 billion letters can have massive consequences.
Added to that fact we all have many differences between our genomes that make us unique.
The idea of reading a genome and deciding what is and isn't human in evolutionary terms is a pipe-dream.