Apocrypha changes nothing. Everyone (even the Christians who use it) recognize it as not the same as canonical books of the Bible. A look at the history of it, the manner in which Jerome and other early translator included with their translations of Scripture but not as Scripture only as other "good writings" as well as the exclusion of Apocrypha from lists of canonical books in the early church, not even to mention the contents of the Apocrypha, which I agree are not entirely harmonious with the Bible.
As far as the 99% commonality--I have studied the entirety of the Gospels in Greek and a majority of the Epistles in Greek, my studies in Hebrew are not as extensive, but I would estimate I have read 30-60% of the Old Testament in the original. I have found maybe 2 cases where the manuscript evidence was not clearly in favor of a specific reading of the original and where the difference changed the meaning of the passage (99% of differences are 1 letter, a past tense or present tense, the word 'said' vs the word 'speak' or other minuscule things that in a less important document would be totally ignored). Even in these cases, where the meaning of the specific passage could be changed, the unified teaching of Scripture was not affected by either possible text.
Secular work on the Bible usually has an axe to grind. But usually the difference isn't the translation of the text itself but rather the idea that there is a different, older text that we don't have that we have to get at through cutting and pasting the existing text. If I have missed your point, please provide specifics and I will be happy to respond to them.
Also, I followed your link. Is your suggestion simply to engage in discussion on that forum or was there a specific thread you felt would benefit me?

