One of the most significant changes is that he is humbled, and finally realizes that Finny was not out to get him, was not competing with him, and did not hold sinister intentions for him. Gene had been jealous, and angry at Finny, assuming that Finny was undermining his studies, and competing with him constantly. But, as he talks to Finny in the infirmary, he realizes,
"And I thought we were competitors! It was so ludicrous I wanted to cry."
So, he has that revelation, and it is hard for him, because now he realizes that he hurt an innocent person who didn't in any way deserve it.
Secondly, Gene is introduced, hard-core, to guilt. He feels so guilty for what he has done to Finny; it is a pervasive emotion that weighs on him and becomes his defining characteristic. He states, "I was confronted with myself, and what I had done to Finny," and he walks around in a "pool of guilt". This guilt makes him defensive, paranoid, anti-social, and even violent-he hits Quackenbush, he says, "in the role of Finny's defender." So, he struggles with the awful thing that he has done, and tries to redeem himself from his guilt in various ways.
Lastly, he realizes that he has, from the beginning, wanted "to become a part of Phineas." He owns up to his jealousy. He tries on Finny's clothes and is comforted; he feels "a soaring sense of freedom" when Finny asks him to play sports for him. So, he realizes how jealous he had been, and that he envied Finny so much that he actually had wanted to be him.
These are some difficult realizations and changes for Gene in these two chapters. I hope this helps a bit! Good luck!