Question...

A few days ago I went to the library in an effort to follow in my more philosophically-minded brother's footsteps and read The God Delusion. I am interested to see what he says, as I have heard him described, albeit hyperbolically, as the greatest thinker of our time. Unfortunately, the book was checked out, and so I settled instead for another book by Dawkins, entitled The Selfish Gene. I am probably about 3/4 of the way through it, and so far it is interesting and I have had almost no major disagreements with what he says. He focuses on evolution with respect to the genes of an individual (his catch phrase is the "survival machine", manufactured by the gene to facilitate its replication), and appears to be able to explain the theory pretty well as far as I can see. I do, however, have one big question about evolution which I have not found in his book thus far, which perhaps someone might be able to help me with. Natural selection is pretty much a universally accepted principle nowadays, and it seems perfectly sound to me - using Dawkins' language, genes which produce flawed bodies would fail to reproduce themselves and become less numerous in the gene pool, while genes producing fitter bodies would become more numerous. Eventually the unfit ones would die out completely and the species could be considered to have evolved.
The problem with this is the enormous complexity that we observe in the world. Evolution can explain species changing, but it does not seem to explain them growing more diverse. In fact, Dawkins himself points out that genes which fail to replicate themselves perfectly would become less numerous in the gene pool. Natural selection does not account for variation, it should actually eliminate it.
Suppose an animal's (say, a giraffe's) habitat is suddenly changed in such a way that only by having a long neck could it survive. We are inclined to say that the species develops and "evolves" a longer neck, but this is not how it happens. In reality, giraffes with short necks die off and giraffes with long necks live. This is the essence of natural selection. While we could say that the species "evolves" a longer neck, all that really happens is that the average neck length increased, because you killed off all the animals with short necks. The genetic makeup of a giraffe did not really evolve; that's like saying a school gets smarter when the stupid students drop out. No individual student will get smarter - it is only the average which increases. In the same way, a giraffe's neck could not get longer because giraffes with short necks died out. The giraffe could only have developed its long neck if there existed, prior to the need for a long neck, at least one individual of each sex within the population with the long neck that we see today. After the change, all the other giraffes would die and only these relatively few would be available to "rebuild" the species in their own image, namely, that long neck. But that neck would not, barring extremely fortuitous genetic mutation, be longer in the next generation than it was in the previous.
Natural selection can take advantage of an existing variation within a population to change the average genetic makeup of that population, but it cannot actually perform a feat of evolution as it is purported to have done. Proponents of evolution then seem to be left with random mutations to provide this variation which natural selection can then choose between. It is my understanding, however, before reading Dawkins' book, that mutations are incredibly rare and random occurrences which are overwhelmingly more likely to harm an animal than help it anyway, and in addition, Dawkins himself seems to say that gene mutation should decrease through evolution, as it is only genes which replicate themselves to the most reliable extent possible that persist through the ages.

Anyone care to explain this discrepancy to me? I may not have much respect for Dawkins, but too many other learned people are staunch supporters of evolution for me to dismiss it readily. I feel as though I must be missing something.