Most of us don't keep our cars stock. We're Mustang owners, and therefore, we're car guys. We're going to mess with our cars.
Most of us even turn our own wrenches, and know our way around a shop manual. But a Chilton or Haynes manual is meant for the stock car, it doesn't do you much good once you start throwing aftermarket performance parts at it, and most of those parts come with their own instructions, how is one going to keep track of it all?
It's easier than you think. Buy a notebook and some document sleeves, and you can turn that mess into something like this:
It starts with my original build sheet (safe place to keep it, and I've got it for reference), then continues on with every piece of documentation I have for the mods on the car (not all of which are pictured here for the 10-picture limit, but you get the idea.
When the car is finished, I'll keep the notebook in the trunk with the tool kit and the Haynes and Chilton manuals. This way, in the event of a roadside emergency, I've got the info on how to troubleshoot my EFI system, ignition system, how things are supposed to be wired, etc. handy!
I also keep a small notebook with part numbers for the things that aren't mentioned in the tech guides that came with the performance parts (things like the serpentine belt I run, what radiator hoses, which spark plugs, etc.)