Blotty: It was emphasized over and over the name [divine name, which ever form you prefer] would be "known" (other words used aswell) Forever
If this is the case, then there is no cause for concern: God would make sure that the divine name would be known. And if it was that important to Him, He would make certain that it was pronounced as He intended. (And if it's not the right God, then the whole thing is moot.)
Otherwise, I am not sure if there are any manuscripts that are considered as a source that is used above all others to determine such matters? If we lack the original writings, then we are going by copies (and in many cases, copies of copies etc). Without some sort of rules for how to organize them, I guess one could go with the model that is most prevalent. But even that has issues, since many manuscripts are incomplete and some are just fragments.