I have gone through a struggle in some ways like yours. I came to realize that the Bible cannot be read literally. If one does that, then one must explain away all manner of contradictions. It was a crisis of faith for me. But as time has gone on I have come to love the Bible in all its poetic imagery and stories and lessons. It has become more meaningful when I have come to realize that I do not have to believe it literally, but I can read it for the meaning that God has for me at this place and time. I grew up in a very conservative denomination which spelled out everything I was to believe. It was easy to believe what was handed to me, but it is much more meaningful now when I can say, "God I do not understand much about you, but it is OK that I don't." To submit my faith to God and not to rely on what someone else tells me to believe has brought me closer to God.
My church, the Episcopal Church is generally quite gay-affirming and is a place with a strong emphasis on the Word of God and the work of God in our lives. I recommend the Episcopal church to everyone. I also know some very supportive Lutheran (ELCA) congregations. Those two denominations are in most areas.
A great book on the Bible and Biblical interpretation is The Good Book by the late Peter Gomes.
Your son is fortunate to have a father who is loving and accepting. Too many gay youth have had to face life without that support. I pray for God's blessing on your spiritual journey.
(I am always willing to talk if you ever want to PM me. I do not visit the forums often, so I miss much of what goes on.)
For I am convinced that neither life nor death...neither the present nor the future nor anything in all creation will be able to separate us from the love of God that is in Christ Jesus our Lord. Romans 8:38-39