Please pardon my stating the obvious, but it seems that there are only two possible categories of answers here: either you do it the way everyone else does - i.e., standard project management techniques appropriate for the level at which you do your work - or you do things your own way and invent your own methods. Following your own path is great stuff, but there are always costs to doing so, many of them unpredictable or at least invisible from the point where you diverge from standard practice. Take it from a guy who's climbed a lot of strange mountains and sailed many a mile of stormy seas, both literal and figurative, for the last few decades: when you choose to be different, you need to be very, very careful about picking your battles. E.g. - sure, you like doing this your own way - but what are you willing to pay for it in time, effort, money, and trouble? Figure out that limit, and revisit that decision once in a while.

What I want is nothing less than a single, coherent guide to project management: How to organize files in my local project folder and how to get them from there to everywhere else they need to go.

Expanding on and continuing what I've said above, I don't think that the answer you're looking for exists - at least not in any way that can be conveyed in a post (or even in a thick book); the situation is complex enough, and constrained by enough of your personal choices that the solution is going to be primarily social rather than technical.

You could learn project management techniques - there are academic courses available for this - and design your own system (and continue to revise it until it's exactly what you want); this is perhaps the most scalable solution. Conversely, you could hire an experienced project manager (heck, there's probably tons of them starving at Dice.com) on a consulting basis, feed them your list of requirements, and ask them to design a system for you. Since you won't be the expert in the situation, *listen* to their advice about the pitfalls if you go this route; I understand that you want to do things your own way, but there are times when certain techniques are just B.A.D. (Broken As Designed) from word 'go', and need to be done away with.

In any case, as one explorer to another, I wish you the best of luck. :)