Your numbers are wildly wrong. I'll do them correctly for you.
The human genome differs from the chimpanzee genome by only 35 million base pairs, of which about 5 million are thought to be active. Compare that to the total genome of around 3 billion base pairs.
So disregarding the inactive mutations, there needs to have been time for about 5 10^6 beneficial point mutations to take place. That's all.
The rate of point mutations is roughly 100 per birth. After a few hundred generations, any beneficial mutation will spread throughout the genome. So if it has been 5 10^6 years = 2 10^5 generations since humans and chimps diverged, 2 10^5 * 100 * N mutations have occurred, where N is the population size (taken to be constant for simplicity). You took N = 10^9, which is obviously too high - let's take it to be 10^7. Then we have a total of 2*10^14 mutations total in the human genome since the time we diverged from chimps.
Of those, 5 10^6 active ones remain. So in order to explain the divergence we need that the rate of beneficial mutations in humans/chimps be around 1 in ten million. That is very low, but it might be about right.
This may also allow us to estimate the rate of neutral (inactive) mutations - naively very roughly 1 in a million (all the rest being harmful). However the logic applied to neutral mutations is a bit slippery.