Q#1: Mutation is essential. It's the only way a new trait can develop. It's basically a starting point for a particular trait or a change to a trait. Most viable mutations don't affect the phenotype at all. As mentioned, they'll occur in dormant sections of the genetic code, which end up doing nothing. The ones that do change the phenotype aren't drastic. It might turn off, say, the growth gene on a tail earlier than what it's done in the species in the past, leading to a shorter tail. This, for whatever reason, turns out to be betted suited for an individual of that species to reproduce, and so that trait begins to be more prominent in the population. After 600 generations, say 2000 years, you now have as many short tails as you do long tails.
That is simplistic and I could go on, for instance, the long-tails and short-tails end up not breeding with each other and over a span of time, say 10,000 years, the long-tails and short-tails can no longer produce reproductive children. Now we have two species instead of two. Pretty impossible to tell where and when the split occurred, especially when you may find one or two fossils of these species. All you know is what it used to be 12,000 years ago and two different species now.
Q2: There is no pretending. Survival of the fittest DOES NOT mean natural selection. Firstly, evolution is about reproducing, not surviving. Secondly, there's absolutely no way to define "fit." Whatever "fit," may be is under constant flux, so it doesn't even matter if one is "fit" for whatever environment it's in. That environment will change.
Q3: Darwin had no knowledge of the genetic code. He also had no real concept of anything outside natural selection, like genetic drift. He also didn't understand the gradual change in species over time.
