(eNotes editors may only answer one question per post. If you need more help, please resubmit other questions separately.)
Gene is surprised, pleased, and slightly uncomfortable to find Finny in the dorm room when he enters.
Gene is surprised because he didn't expect that Finny would be able to return to Devon for some time yet as he recovered from his injury. He was pleased because he recognized that Finny was happy to be back at school and because he could see that Finny was physically feeling very well - "I had never seen an invalid whose skin glowed with such health."
Gene was somewhat uncomfortable because he was still struggling to understand what had happened at the tree and how he felt about the accident, about Finny, about himself. Gene didn't know what Finny's understanding of any of those concerns was, either, until the next morning, when he gained insight into Finny's feelings after Brinker asked Gene if he was ready to go enlist.
He needed me. I was the least trustwrothy person he had ever met. I knew that; he knew or should know that too. I had even told him...He wanted me around.