That's a lot of stuff! I don't have a very clear idea of what you're describing, so 'll answer what I can and hope that it covers what you need.
1. Avoid the slider - it's not worth it even for your best direction.
2.If the head of the bed is split, you would need to cover the window with thick curtains while you sleep.
3. Yes, it is much better to face the entrance.
4. Diagonals - tricky one. I believe Marie says they are fine. I would say they are fine provided you have very good, solid headboards. My experience is that the thin headboards many people have are insufficient to deal with the space that is created between the bed and the wall when you place them diagonally. Give it a try though, you may find this works for you.
5. The beam - move your son's position if at all possible. If not, place a hanging that curves gently around the beam to disguise its presence. It won't fully neutralise the effects, but it will certainly soften it. This might be your best bet since you will have the space to do it, with the high-vaulted ceiling.
Best of luck!