Atfer Gene jounces the limb, he hears Finny hit the bank with a thud. Why does Gene jounce the limb? What were his thoughts about himself and Finny just prior to the jump?

I think  that Gene meant to frighten Finny, but I do not think it was his intent to hurt him. Their relationship was very passive aggressive. Their rivalry and affection for each other became tangled into a mass of teenage angst. Gene shook the tree limb but was not fully aware of why he was doing it. He certainly did not mean to cause that kind of damage to Finny.