sechel, I believe it’s in Toldos Yakov Yosef on Chukas, and Noam Elimelech on Balak.
There are plenty of things that the Besht taught that were new. Changing things so that learning Torah was no longer the main avodah. Proclaiming the primacy of d’veykus over all else, to the point of ignoring hilchos zmanim.
As for your question of “what’s the issue of not following mesorahs”, that actually comes way closer to apikorsus than anything I’ve ever said. In Judaism, Mesorah is everything. No, the Gra did not change Mesorah.
What is Mesorah? It is the tradition that is passed down from parent to child, from Rebbe to student. If someone’s father does things which are wrong, no, you shouldn’t follow it, because his actions are not from a Mesorah. If there is something where you don’t have a Mesorah from a parent, then you follow your Rebbe. (I don’t mean a chassidic Rebbe, I mean the person who taught you Torah.)
The Besht claimed that he learned his new ways from Achiyah haShiloni, and also that Mashiach told him that when the whole world followed his teachings, Mashiach would finally come. Torah was given at Har Sinai to all the Jews, because only through a mass revelation could it be truly believed. We don’t believe in someone speaking with a Navi who died thousands of years before, and coming away with a new way of serving Hashem. The ways of serving Hashem were there from Har Sinai, and were passed down through the generations. Torah doesn’t change. Not even the Besht could change it, and to believe he could is apikorsus.