I'm a little late to the game here, but I have a small issue with the above.
I don't think it is accurate to estimate the size of changes in such a manner, as there is an enormous complex of transcription factors that create interplay between small changes, ones of which we may never see any actual trace or are located outside the genome that affect the genome. SNPs are important (such as those in FOXp2) but not the be all end all factor for those expressions as well - epigenetic factors can drive selection just as effectively as chance mutation creates advantage. Two sides of the same coin, so to speak.
The HARs in question are not only genes, but some of them are connected with multiple sections of the genome in this capacity. They carry with them effects and reactions that are hard to calculate as single instances of information (bit encoding). Activation of some factors may lead to activation/deactivation of other factors. This networking is far too massive to make sense of without intense inquiry (which assuredly they are doing with GWAS on the 250 HARs mentioned above). Which leads to my inquiry - how is it 25000 bits of difference? We did not see the pathway that effectively created that hardware, and much of it could be conceived as data that is environmental - which is what I suppose you're getting at somewhat, but your rote calculation seems to contradict. Do you simply mean, brain development programs in the actual code? I dont think that is as useful of a perception, as it limits the frame of reference to a small part of the puzzle. Gene expression is much more affected by environmental stimuli than one might perceive, feral children being an interesting point to that regard.