The one thing I truly dislike about linux is the way the system is organized. What I want to do is restructure the system files into something I like. I am fairly experienced with the working of linux, but not so much in the core system sense, so I need a distro with very verbose, detailed, fully commented code.

I have found some of the code in Pardus (turkish linux) is very well commented, giving a very clear image of what the code is doing. I will also be using this as a means to take my knowledge of bash to the next level.

I will give more details on my project as soon as I get it started, but the main idea is to make a more centralized system... It should make automation of certain tasks more simple, at least for me. I was raised with windows, so, if all goes well, this could mean a more clear structure for windows migrators.

Hard to describe in words without actually doing it, especially since my english isn't that great
In any case:

Any distributions you can recommend?

I'm not going to recommend you one. Just try some. With respect to your "idea", well, we already have one distribution with a wonky directory structure (Gobolinux) and we already have a "registry" database (registry.sourceforge.net), so for you to take it to the next level with "a more centralized system", I mean, sure. I do hope you'll come to your senses though. Get well soon! ;-p