His name shall be?

John is John and Jesus is Jesus while Emmanuel is really a title. You may have confused Joseph with Zechariah, the father of John the Baptizer. John and Jesus were cousins. I hope this helps.

You are confusing John the Baptist with Jesus. Zacharias was the father of John the Baptist, whose mother was Elisabeth. Jesus' mother was Mary and his adopted Father was Joseph. When the Angel Gabriel appeared unto Mary and told her she will conceive and have a son, Mary said to the angel how can this be seeing I did not have any relations with any man. Then Gabriel said to her the Holy Spirit will come upon you and the power of the Highest shall overshadow you and you will conceive and bring forth a son and shall call his name JESUS Luke 1:31.

As you read that the angel was first talking to Mary. She is told to name her child Jesus then when you keep reading and get to verse 57 it is now talking about Elizabeth. Her and Zechariah called their son John. You are reading about two different families.

Only the parents shall name him

The biblical incident you are talking about refers to the birth of John the Baptist not Jesus. Jesus' birth is also recounted in Luke's Gospel. Two different stories about two different babies.

I am not sure what you are doing. You missed something in the narrative.