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I wanted to comment on your musings about the organization of the retina. In your post you said:

"This gives me the confidence to think, because we do not understand why the retina is organized backwards, it is likely due to a limit of our methods of research and understanding. I think the retina is organized backwards for logical reasons that we are not yet capable of understanding because I feel like everything in the brain was thoughtfully and purposely arranged."

In response I'd like to mention something else:

The larygeal nerve is a branch of a cranial nerve and gives control to the voice box. In mammals the nerve starts in the brain (of course), loops down and around a ligament of the lungs, and then finally makes its way back up to the larynx where it serves its purpose. Frankly, this arrangement is stupid. In giraffes it means that the nerve has to be about 20 feet long as opposed to about 1 foot. So why is the nerve arranged like this? Well, I'll tell you. Mammals evolved from fish-like ancestors that are morphologically very similar to modern-day fish. In a fish, the position of the shoulder girdle makes the pathway for this nerve a straight line from the brain to the larynx, and it happens to pass behind a ligament of the swim bladder on the way. As our fishy ancestors evolved into terrestrial beings with lungs instead of swim bladders they developed neck regions and this nerve was still wrapped behind that stupid ligament, simply because when the first fish evolved it made no difference at all that the nerve went behind as opposed to in front of the ligament so the fact that it went behind was completely random. However, it just isn't possible to disconnect the nerve and reconnect it in front of the ligament, so it just had to get longer and longer to compensate. Pretty dumb, huh?

I guess what I'm trying to point out is that evolution is completely undirected. It isn't about "what works BEST" its really just about "what works," or even, "whatever happened to come first that kinda worked." I'll be honest that I sincerely doubt that the problem here is that we don't know enough about the eye to understand why it is organized this way, and also, most likely the layers won't ever switch positions, simply because as far as evolution is concerned the current organization is "good enough" so there isn't really a selective pressure that would make any random mutation that might happen to occur (which, by the way is highly unlikely because it would be an extremely complex process to switch the positions of the two layers and the likelihood that a mutation like this would somehow happen, or that any intermediates would be favorable in some way that would even allow the process to continue is virtually zero.) be favorable. Evolution has no purpose, and our brains can’t direct it at will. It has no goal. There is no presentiment on the part of evolution. It is essentially random except in the sense that if a mutation that randomly occurs is favorable, that individual might stand a better chance of surviving and reproducing. Or it might get eaten the day after it's born. That’s why this stuff takes millions of years and you still get bats with solid bones instead of hollow ones like birds. Its just plain random.