Hi, I'd like to help you with your question.
It sounds like your son may be in mourning over the loss of his father. Children can go through the grief process over losses of any type. Even with his father being so accessible, your son probably misses having his parents together and the family as a unit. It is hard for a child at his development age to understand why parents cannot be together and why he cannot have his dad with him at home.
Grief symptoms in a young child include exaggerated fears, lack of concentration, and sometimes mood swings. Withdrawal, tearfulness and sleep problems can also occur.
Consider having your son see a therapist. Although the Reiki therapy may help, your son needs to see someone who can identify his grief symptoms and help him express his feelings about his loss. A child therapist usually uses toys to help children, whose vocabularies are not as large, to express themselves. You can ask if your son's father can participate to help your son.
There are some books that may help you and your son. One is called The Truth About Children and Divorce: Dealing with the Emotions So You and Your Children Can Thrive by Robert E. Emery. Books to help your son are Standing on My Own Two Feet: A Child's Affirmation of Love in the Midst of Divorce by Tamara Schmitz and Two Homes by Claire Masurel and Kady MacDonald Denton.
You sound like you are doing a great job helping your son. With a little time and some therapy, he should adjust and do very well.
I hope this helped you,