What are the "internal confilcts" Jerry is facing?
Initially, Jerry is conflicted about whether or not he should leave his mother alone. He desperately wants to go to the "wild bay" and leave her at the "safe beach" that they always visit. Once she senses this, she offers him the opportunity to leave her, but he declines it the first day and "Contrition sent him running after her." He feels a little guilty about wanting to leave her. His "contrition" is again referenced the next day, as is his "chivalry." He feels responsible to and for her, perhaps in part because she is a widow, but he also really wants more independence and freedom. He is very torn between staying with her and branching out on his own.
Jerry's second internal conflict has to do with swimming through the tunnel. Although he sometimes thought that "He would do it if it killed him [...]," but in the next moment, "He thought he would return to the house and lie down, and next summer, perhaps, when he had another year's growth in him -- then he would go through the hole." Jerry recognizes the danger in attempting such a difficult feat; he very literally could drown in that tunnel. However, he also wants to do it anyway. He would prove something to himself in accomplishing it.
"But even after he made the decision, or thought he had, he found himself sitting upon the rock and looking down into the water, and he knew that now [...] -- this was the moment when he would try. If he did not do it now, he never would."
He hemmed and hawed for quite a while, and though Jerry shook with fear and dread, he finally did do it.