Hi,
My 6 months old daughter just went through a period of night waking and is now sleeping through the night again. I hope my solution will help you as well.
My daughter has always been a good sleeper. For the past 2 weeks, she has been waking at 4:30-5:30 am crying and refuses to go back to sleep. It's a long story and took a while for me figure it out. In short, she was waking up due to the coldness in early morning. I had thought she was warm enough with fleece onesie, fleece swaddle, and 2 thick blankets, but apparently she was still cold. I added a thick sleeping bag for her three days ago, and she had been sleeping through the night again since. Hindsight, her little body cannot hold a whole lot of heat to keep her warm through the night. Your son might have been waking due to early morning coldness. Good luck. Hope your son gets well soon.