To what was Gene referring when he states that he again had the feeling "of having all along ignored what was finest" in Finny?

I think it was the scene of Finny needing help from others. Finny was a person larger than life. He was the one who helped others, not the other way around. Finny was a bright star which should burn out, not fade away. Gene also understood that his own role was not "helping" Finny,

"I didn't think he knew how to act or even how to feel as the object of help. . . My aid alone had never seemed to him in the category of help. . . Phineas had thought of me as an extension of himself."