Have you included the probabilities for these mechanisms somehow randomly forming, in your calculations. For example, these mutations are not just from a random number of bases combinations passing by and accidentally falling into place. The transcription errors, and then the corrections, also fall into the overall probabilities. These things reduce the likelihood of beneficial mutations even further. In addition, what we call a beneficial mutation is subjective many times. What is beneficial to a worm, would not be beneficial to a cheetah. And vice versa. Or in another case, something that is less beneficial, may still survive, because the environment is large enough for several options. As in the same environment may be able to support both white-tail and mule deer and elk and woodland caribou. There is no real distinction about what is more or less beneficial in this case.
Ironically, if we assumed human evolution from some hairy ancestor, we would see that in order for the benefits of a bigger brain to be advantageous, it would have to be accompanied by a weaker body, and by hairlessness, a vulnerability to weather. Otherwise, there would be no need to use the bigger brain to survive, and thus no advantage to the bigger brain. The hairy human with powerful hands and feet and long tail could simply survive in the open like all the hairy apes, instead of wearing clothes, building houses, growing gardens, and herding sheep.