“The Litvishe Mesorah does not go back thousands of years.”
The Ashkenazi mesora does. As I’ve pointed out before, nobody other than wikipedia editors actually mean “Lithuanian” when they say Litvish; it just means non-Chassidishe Ashkenaz.
“But the more we go back through the last millenium, the more we find even larger differences among the European Congregations.”
This is an important point. Many of the differences between what we consider nusach Ashkenaz and Sphard were just pre-existing differences in Europe. Eg. saying “sim shalom” not “shalom rav” is brought down by Ashkenazi poskim, the placement of shir shel yom before aleinu, the inclusion of “Hashem melech” in psukei d’zimra. The only major chiddushim were changing the nusach of kedusha, and placing baruch sheamar in the middle rather than the beginning. Most of the other things have a basis in some version of the Ashkenazi mesora.
All this being said, I think I still agree with DaMoshe’s underlying point: just because there were divergences between towns in Europe doesn’t mean people can just go and start inventing their own minhagim based on sectarian hashkafa. The minhagim that people have criticized on these forums are exactly that.