And it is all in how you accept the rewrite of John's back story. Reilly played havoc with Days characters. John's history has always been that Daphne DiMera gave birth to John, who was the result of an affair she had with another man. She gave him to her her sister to raise, and he was named Forest Alamaie. Lawrence was a bit jealous of Forest, there was a pool accident, and his mother sent Forest away to boarding school, with vivian being the only one who knew. Eventually Stefano learned of this, got hold of John and thus began all the experiments with his brain and memory, holding him hostage, Rolf in the lab, etc. John thus became a priest at some point, was in the art theft business with Princess Gina....and eventually brainwashed and given Roman Brady's memories. He was given a host of abilities, memories, etc.
As to Shawn Brady's sister. She left her son in an orphanage, and was unable to learn what couple took him. She eventually settled on the Alamain family, who knows for what reason. I really loved Shirley Jones in the story, but as far as I was concerned, she was mistaken, John was not the son she lost. Heck, Tony DiMera & John had the same mother, and had tests to make sure. And Tony is NOT the bio son of Stefano.