File organization is paramount. Have a place where old versions go so you can easily revert, but make sure all of your new files are together without any old ones sneaking into the folder.
Your points reminds me the numerous rereading of rules, cards, player's aids, and boards I was part of for Robotech: Reconstruction to counter the problems you highlighted . On my end I was dependent on spreadsheets of what to check to help make sure nothing was missed. The other thing we did was create a document separate from the rulebook to define terms and how they were going to be used to both ensure consistency and serve as a que that a change would have an impact across the rulebook and components.
Another one to add might be to have other people with fresh eyes look over the wording on your components and in the rulebook. This can admittedly be hard to find since the majority of people are not great at writing, editing, and so on. I would even say it's worth it to pay someone just to be sure. Looking at the same thing for long periods of time can often blind us to little mistakes. The first game I worked on I ended up wearing MANY hats for a variety of reasons: I did the art, graphic design, and print layouts, which required me to also do be an proofreader/editor. I am an fairly skilled in all those areas, but even still, somewhere in the process I missed one word in the rulebook before shipping the game files off to be manufactured... at the very end of the book, on the last page, on a separate line below the last paragraph is one single word: "Ignore" At the end of the day it wasn't catastrophic but it was still EXTREMELY embarrassing. And even though everyone on our team was supposed to also go over all the files to look for mistakes before shipping it off to print, I still felt like a total moron since I was so massively involved in the creation of all the assets. If we had handed it off to someone not so intimately tied to the development, they likely would have spotted that mistake.
