Ray Birdsey is a veteran of WWII and Korea, who marries Concettina Tempesta, a woman with two illegitimate children from an unknown man. People thought Ray was a saint for marrying a woman who already had two kids, which today would be like someone with PhD in Physics taking a job at Burger King. Or something like that. During their childhoods, though, Ray was often angry and abusive, directing his rage at Thomas, whom he thought was too feminine and sensitive. He probably thought he was toughening Thomas up.
Dominick spends a lot of time trying to rationalize the abusive Ray of the past with the comparatively nice Ray of the present, but we're tired of talking about Dominick, so we'll focus on Ray.
Ray is also conflicted with the way he treated Thomas. He, too, wonders if the way he treated Thomas aggravated the boy's mental illness. Unfortunately, he can't go back in time and change things, so all he can do is try to be nice to Thomas in the present. He starts calling Thomas "my kid" (3.150), taking ownership of him in a way he never did when Thomas was a boy. And when Thomas dies, Ray plants beautiful tulips near his grave.
As a man who has seen war, Ray knows that all he can do is try to come to terms with the horrors of the past, and set things right the best way he can. Unlike Dominick, Ray understands there's no going back.
Just like Dominick is "amputated" from Thomas, and Thomas amputates himself from his own hand, Ray also experiences an amputation of his own: he loses a leg. Throughout the novel, Ray mentions numbness in his feet and leg pain, but he mostly ignores the problem. Dominick ignores it, too, because Dominick tends to ignore anything that doesn't have to do with himself.
Ray ignoring his own pain until it's too late is typical of his MO. He did the same with Thomas, abusing the kid on repeat until Thomas broke and couldn't be put back together. And similarly, Ray ignores his own diabetes until his leg has to be amputated.
But this amputation is also a source of connection, bringing Ray and his surviving "son," Dominick, closer together. Dominick realizes that Ray isn't the same angry man he used to be, and he starts taking care of Ray, bringing him to the movies, out to eat, and helping him to shave. The moral of this story: If you need to make a change, cut off a body part. Okay, um, don't try this one at home.