S.,
With the length of time that this problem has gone on, and the fact that you have already tried EVERYTHING that you have (taking him to his room, sitting with him to calm his fears, sleeping on the floor of his room, etc.), I believe that professional counseling is in order for your son. Some years ago I might not have suggested this, but I NOW have experience that makes me think that, for ANY ongoing issue, "the earlier resolved, the better."
I am married to a man who, in his late 40's/early 50's, had to deal with issues stemming back to his childhood. Thank God we discovered a marvelous Christian counselor who served as an inspired guide to help sort out how his adult behaviors related to childhood incidents and issues. My husband is 100% "A-OK fine!" now; but if certain of his beliefs and fears had been dispelled at a much earlier age, when they were occurring and fresh, he would have gained 30+ years for more successful and peaceful living. I'll be happy to provide you with contact information for this counselor. Just email me, if you want the info.
Not the least of the problem is the impact of fear on your son. I totally agree with your husband's feelings that the master bedroom is no place for your six-year old. Whether you are cognizant of it or not, having a child sleeping in the bed/room with you, or very possibly bursting through the door at any moment, WILL eventually have a negative impact on your sex life. Perhaps the situation already has a negative affect upon your intimacy, even if current affects are only the result of exhaustion and worry. A master bedroom should be a "haven" for couples, where both are free to be intimate and romantic at any time, without fears of intrusion.
As a Christian, I also believe it is important for your son to know that faith in Jesus, when totally actualized, removes all fear and produces perfect peace. If you are a Christian, you may already know this and simply need to discuss these things with your son. Using Bible verses and stories to help him know how to form and depend upon that relationship with Jesus will transform his life. If you and your husband are not believers, then seeking and developing a relationship with Jesus Christ is paramount for you, such that you both have a basis of peace to convey to your children. Perhaps the verses below will help:
1 John 4 (whole chapter, including...) - "...but perfect love casts out fear..."
John 14:27 - (Jesus words) "Peace I leave with you; My peace I give to you; not as the world gives do I give to you. Do not let your heart be troubled, nor let it be fearful."
Romans 15: 5-6, 13 - "Now may the God who gives perseverance and encouragement grant you to be of the same mind with one another according to Christ Jesus, so that with one accord you may with one voice glorify the God and Father of our Lord Jesus Christ...Now may the God of hope fill you with all joy and peace in believing, so that you will abound in hope by the power of the Holy Spirit."
Luke 1:76-79 - (prophecy about John the Baptist as a forerunner of Jesus) "And you, child, will be called the prophet of the Most High; for you will go on BEFORE THE LORD TO PREPARE HIS WAYS; To give to His people the knowledge of salvation by the forgiveness of their sins, because of the tender mercy of our God, with which the Sunrise from on high will visit us, TO SHINE UPON THOSE WHO SIT IN DARKNESS AND THE SHADOW OF DEATH, to guide our feet into the way of peace."
Matthew 19:14 - "Jesus said, "Let the little children come to me, and do not hinder them, for the kingdom of heaven belongs to such as these."
Blessings,
K.