You asked how we get from light-sensitive cells to a mammalian eye. In terms of phylogeny, the phenotypes organize rather neatly along that path. Of course it's a gross simplification - web boards are not generally conducive to book-length theses, and my time would not permit me such an indulgence in any case ;)
If you would like more detail, I am sure that I can find some more in-depth material to suggest to you. However, since you have asked a few specific questions, I will try to answer them as best I can.
For example, what benefit is any kind of "lens" before the eye is fully functional?
Ah. At what step, precisely, that I propose, is there an eye that is less than fully functional?
And where is the co-evolution of the central nervous system in all this? An eye is useless without a CNS.
Insects have eyes without a central nervous system. But the question is a valid one. You should have asked it instead if that was what you were really interested in ;)
More seriously, as the resolving power and level of detail that eyes are capable of perceiving increases, there is indeed a rise in nervous system capacity as well. Which isn't particularly surprising - what good are superb eyes without some means of interpreting and making sense of what you see? And, of course, that's just one of the many functions of our complex and highly developed brains. But complex and highly developed brains like ours are not a requirement for superior visual acuity - many birds, for example, have very complex and well-developed visual cortexes (and finely tuned eyes, of course) that permit them eyesight that far exceeds our own. But if your eyesight is not even in the same league as an owl's, neither is the owl's brain in the same league as yours.
Yes, some development of a nervous system is necessary as eyes develop also, but I don't recall claiming otherwise.
More than useless--wasted resources that would be selected AGAINST.
Why? Why do men have nipples that are apparently completely useless?
You come closer to your real position when you say that just because something cannot be understood now doesn't mean it isn't true.
That is not my position regarding evolution. In fact, if you go back and re-read my post, I think you will find that what I say is that just because you cannot understand it does not mean it isn't true. And I suppose I should add that it also does not follow that if you cannot understand it, no one can understand it ;)
You have your faith; the UFOlogists have theirs; the theists have theirs. Darwinism rests on a secular materialist faith.
I think not. Like all inductive arguments, it establishes probabilities of truth, not absolute certainties. Nonetheless, we all accept as true all sorts of things that cannot be logically proven true every day of our lives. The question is not "can it be proven true?", but rather "is the bulk of the evidence falling one way or the other?" And it is.
Evolution via natural selection best explains the evidence before us, far better than any alternate explanation. I find it highly unlikely that a competing theory will muster sufficient evidence to displace it, but it would be foolish to forever foreclose the possibility.
It's not science--at least not yet.
What about it do you find unscientific?
The big question for biological science in the 21st century is WHERE this software comes from.
Setting aside for a moment the question of whether software is an apt analogy, I think that a naturalistic explanation is more than sufficient.
Really, I think we're getting at the crux of your objection, so let me make some preemptory statements here. First, finding evolution via natural selection to be a compelling theory for the development and diversity of life on earth is not a priori incompatible with a belief in the divine. Even among scholars of evolution, Richard Dawkins is an anomaly insofar as he is a militant atheist. At worst, what evolution via natural selection is incompatible with are certain very literal readings of the Bible. And conflicts of that sort are really quite easy to avoid in the first place if we accept that God might occasionally speak in allegorical or metaphorical terms. ;)