SPOILER-The one piece of the jigsaw that will make you understand it all
Joshua was seeking the approval of his father.
Joshua's uncle was his real father.
The uncle confesses this in a veiled manner when he says that mental illness runs in his family.
Brad was a loving father to Joshua (who he believed to be his own biological son)and to his daughter.
Brad felt the disconnect between himself and Joshua and was trying desperately to strengthen the bond between them and felt himself failing miserably.
The psychotic behavior of Joshua was passed down from his mother and father. He was twice as disturbed of his mother and father/uncle since both contributed to his nature.
He also gave a clue when Joshua talked about the father not being able to love him as much as mommy was able to.
He was not talking about Brad but instead talking about the uncle.
The mother was able to publicly present herself as his mother because she physically gave birth to him. The uncle had to hide the fact that be was Joshua's father and give up his father role to Brad.
Joshua being doubly psychotic as his mother (being a product of incest between two psychotic siblings) he messed with her medications to bring her back to his level of insanity.
Joshua also had some resentment towards his mother for not being faithful to his uncle/father.
You could also see the comfort the uncle had with being around and holding his sister as she breast pumped. This was meant to further show that they were used to being intimate with each other.
Another huge clue was when she was hurt about a comment that made the breast pump sound being unattractive. She was upset as she felt she was looking physically unattractive to her lover, her brother.
Lily was the product of Brad and his wife. This is why Joshua was half connected to her emotionally. He was also at the tipping point of loving Lily because she was his half sister, and rejecting Lily, even to the point of killing her, because she was half the child of Brad.
You understand it now? No plot holes or anything unexplained when you realize that Joshua is the son of his mother and his uncle.
This is Brad's tragic story about how he believed the the son of his psychotic wife and her psychotic brother was his own son and how Joshua hated and destroyed him to be with his father/uncle father.