Yosefcoleman, your question is better than any answer you will receive. I’ll try to put things into perspective.
Before the ashkenazic influx, the minhagim were indeed sefardic, but in a loose way. Sefardim are less uptight than ashkenazim and throughout the ages were more amenable to minhagim of others (i.e., the Rosh after 1306 in Spain).Remember that the old yishuv was not technologically or communally advanced. The sefardim did not rule by central authority, which allowed for others to fill a vacuum.In addition, sefardic minhagim are not monolithic, there are many variations there too.
The chassidim who came with R’ Menachem Mendel of Vitebsk in the 1770s were concentrated in Zefat and Tverya and had a
minimal and uninfluential representation in Yerushalayim.
The first talmidei haGra , of the Rivlin family, came after 1809, followed by larger numbers in the middle of the 1800s. As proud bearers of the torch of the Gra, they exploited the vacuum to establish their way as the Ashkenazic way, and hence we have minhag haGra as minhag yerushalyim and by extension, minhag Eretz Yisrael. As Yerushalayim goes, so goes the country. As a historical quirk, all know that minhagei haGra were not accepted in Vilna, his hometown. They were only disseminated decades later and far away.
Needless to say, not all are happy with this system, and the current chassidim never accepted it. Here and there there are pockets of resistance from the yekkes, the Americans, and others who aren’t willing to let go of their old minhagim. We can debate who is right, but that’s irrelevant from a historical point of view.
edited