So, I will focus on the parentage of James.
1. Mark 15:40 There were also women looking on afar off: among whom was Mary Magdalene, and Mary the mother of James the less and of Joses, and Salome;
This is at the Crucifixion. Mary the mother of Jesus was not "afar off" as we know from John; additionally, if she was the mother of Jesus, why not just refer to her as this, obviously, this is the "other" Mary from the Gospels.
2. Matthew 28:1 In the end of the sabbath, as it began to dawn toward the first day of the week, came Mary Magdalene and the other Mary to see the sepulchre.
John 19:25 Now there stood by the cross of Jesus his mother, and his mother's sister, Mary the wife of Cleophas, and Mary Magdalene.
This clearly establishes that there is a third or "other" Mary, the wife of Cleophas, and the mother of James among others. She is probably the Virgin Mary's sister in law or close relative.
Additionally, the second chapter of Matthew clearly indicate that Mary, Jesus and Joseph go into Egypt and only the three of them come out. In Luke 2, speaks of the Holy Family of three going to the temple in Jerusalem with no other children.
In middle east culture, it is unheard of for a younger sibling to rebuke an older sibling and certainly not the oldest. As James, could have been no more than a teenager if he had been born after the journey to the temple, it again makes sense that these "brothers" were older relatives. In Genesis 13:8 and 14:16, Lot is called the "brother" of Abram, yet 11:27 indicates that Lot was Abram's nephew.
Why did the writers of Scripture not make this clearer? Simple, they didn't see the need. This was accepted fact and only centuries later did anyone ever question Mary's Perpetual Virginity. They never foresaw the occasion when this would be questioned. And in fact it wasn't until very recently. ALL of great Protestant Reformers accepted this (I have already posted links to this, so any further ones would be pointless).
Invariably the question then turns to, "why wasn't this spelled out better in scripture?" "God should have foreseen the questions and inspired the authors to spell it out better." To which I offer this for your consideration:
Nowhere in scripture is the Trinity explicitly defined, and probably no tenet of faith is more difficult to comprehend than the Trinity. Wars have been fought, people have died over this controversy, yet the Bible is silent.