I'm in the process of putting together a 4e campaign, and I'm going to be compiling everything I can into a private player reference. I know there are a few iterations of some powers, monster mechanics, skill challenges, with varying opinions on which work better. I'm only operating with my physical books, and I plan to comprehensively compile the classes in one viable structure, so I need to be able to retcon the descriptive texts into one unified chapter progression for character creation. (I'm also planning to explore homebrew when I feel it needed, so the more I understand the system, the better.) That means including consideration for all the later mechanics, like themes, and balance considerations thereof.

Which books hold the best versions of rules? How many iterations of magic missile are there, and is there any benefit to including them as different choices? What's the best monster stat construction, and what other pitfalls are there to look out for when condensing all the mechanics in one place? Any basic tweaks that everybody does? Or common/trusted homebrew sources, or decent 3rd party?

In particular, I'm planning an Eberron game, with a mostly-serious tone established from session 0. I want the campaign to grow organically, with a comprehensive lore codex backing me up on how to fill in the details when I don't have major elements already prepared/known.

Appreciate all the help anyone can give.