This was a really good read, Jonathan. I liked how you dove into some of the books that most of us just talk about.
As far as when the Apocrypha was finally removed from the Bible, I think most Protestant scholars point to the order of the Archbishop of Canterbury (UK) in 1885, but certainly others were calling for their removal before then. But 1885 seems to be the cliff when the books were finally removed.
There have been a boatload of other changes to the Bible as well, some of which I point out in:
10 More Outright Lies the Church Tells To Imprison You