Your longing for fellowship and connection, for laughter and a cheerful heart, for protection and peace in your home, is a tender and understandable cry, and it is good that you bring it to the Father who knows what true fellowship is, for as it is written, our fellowship is with the Father and with His Son Jesus Christ, 1 John 1:3.
There you are, first of all, to be in communication with the Father and the Son and, secondly, to be reconciled to God by the death of His Son, healed of the awful, soul destroying plague of sin. I am persuaded that as you increase in the knowledge of the Father and of His Son Jesus Christ through the revelation of the Divine Spirit, you will also increase your fellowship with the Father and with His Son. When you look at your dear Lord and Master and think of the Father and the Son planning and working with heart and soul for the salvation of the chosen, does not your heart feel intense sympathy with the eternal purpose of the Father and the gracious work of the Savior? If so, you are having fellowship with the Father and with His Son Jesus Christ. Agree to that in your heart of hearts and you will be having that fellowship while you are so agreeing.
Out of that fellowship flows the peace and joy for which you ask. You quote rightly that a cheerful heart is good medicine, Prov 17:22, and that Jesus rejoiced greatly in the Holy Spirit, Luke 10:21, and that the Father anointed Him with the oil of gladness above His fellows, Ps 45:7, Heb 1:9. That gladness comes to us from His fullness, John 1:16, and it is kept in perfect peace. You will keep him in perfect peace, whose mind is stayed on You, because he trusts in You, Isa 26:3. The blood of Jesus whispers peace within. This peace is a present possession and may be enjoyed in the ordinary circumstances of life, even with sorrows surging round and with loved ones far away, for in Jesus keeping we are safe, and they are safe. Bear your sorrow with Him and then see what peace you will enjoy.
You ask for a turning of hearts toward one another, especially between you and your son, Mal 4:5-6, and for a scheduled time for fellowship together, Eccles 3:1, Acts 17:26. You desire training in Bible stories, Deut 6:7, Eph 6:4, mutual respect and honor, Eph 6:1-3, and to pursue peace and holiness without which no one will see the Lord, Heb 12:12-14, with purity of heart that we may see God, Matt 5:8. These are right and biblical desires. The Lord is the better Father than the best of fathers could ever be to the best beloved of sons, and He says, I will be a Father unto you, and you shall be My sons and daughters, says the Lord Almighty. Trust your heavenly Father as a child, for your heavenly Father knows what you require, and you may leave it all to Him. Continue to pray, to worship, to sing, and to teach your son diligently as you have opportunity, whether that opportunity be given through a regular time of video or in such other ways as Providence allows. A king's heart is as channels of water in the hand of the Lord, Prov 21:1, and He turns it whatsoever way He will, in His time and wisdom.
Concerning the three of you and your desire for peace, I must speak plainly and lovingly as a minister of the gospel. Our only peace with God, and therefore our only true peace with one another, is through salvation by Jesus Christ alone, for He is the God of Peace and He has, on His part, prepared everything that is necessary for a perfect reconciliation through the work of His Son. The work of salvation was done forever and on God's part there is nothing now to be removed in order that all who trust His Son may be at perfect peace with Him. He has committed unto us the word of reconciliation because we can speak from experience of the joy which this reconciliation brings. Therefore my first prayer for her, for you, for your boy, and for all who are dear to you, is that each one may be at peace with God through faith in the Lord Jesus Christ, Rom 5:1, for there is no other name by which we are saved and no other ground for adoption into His family.
In that light, I cannot ask God to bless or affirm any relationship or arrangement that departs from His historic and holy ethic, for marriage is a lifelong covenant of one man and one woman, and both sexual union and living together belong within that covenant alone. What God calls holy we must call holy, and what He calls sin we must call sin, trusting that His commands are for our good. If there has been sin, deception, or evil influence, as you fear, Matt 24:4, 1 Cor 8:1, Zeph 3:13, 2 Thess 3:3, then the gracious call is to repentance and to be washed in the blood of Christ, for once in the history of the world has the Son of God appeared to put away sin by the sacrifice of Himself, and when the Father sees His Son bearing our sin upon the cross, it makes such an infinite impression upon His great soul that He remembers our iniquities no more, Isa 43:25. To put such as we were in the same testament with His own dear Son and then to say, I will receive them graciously and love them freely, this is surprising grace.
You mention wisdom, James 1:5, Col 1:9, Phil 1:9-10, and the clause of peace in 1 Cor 7:15. Seek that wisdom not alone but with the counsel of faithful pastors and elders who know you, who can open the Scriptures with you and weigh what faithfulness requires in your particular case. Do not hasten toward separation, for the Lord hates the breaking of covenant and delights in reconciliation, and the privilege of perfect restoration is proffered to you in the gospel. When the prodigal son came back and his father had kissed him, he was to his father as if he had never gone away. His father had him once more at home and loved him as much as if he had never grieved him in all his life. Did not the father give joy to the returned prodigal? There was music and dancing and they began to be merry. And God will rejoice over a poor soul that has wandered far from Him, but at last returns, and the poor soul shall be happy too.
So I pray with you that the Lord would deliver each of you from deception, from sin, from evil influences and evil persons, from temptation and the evil one, Matt 6:13, John 17:15, and keep you from the evil one indeed. I pray that He would grant you protection from imposters and flatterers, Prov 30:8, 2 Cor 11:26, 2 Tim 3:5, 13, Tit 1:16, and that He would discipline you in love as a Father, Job 5:17, Deut 8:5, Prov 3:11-12, Ps 119:67, 1 Cor 11:32, Heb 12:6, Rev 3:19, not to harm you but to make you partakers of His holiness.
Remember Peter's restoration. Peter was down, but he was soon up again. It was brought about by two outward means, the crowing of the cock and a look from the Lord. The Lord turned and looked upon Peter, and that divine look did the deed. That look severed Peter from the crowd. Though the Lord's children go into the far country, they each one in due time say, I will arise and go to my Father. It is not every prodigal that returns but only the prodigal son, and in due time the son returns to the Father's house. If any of us have been falling back and especially if we have wandered into sin, we may get such a restoration from the Lord Himself that we may become better Christians ever afterwards. Till Peter had received from the Lord's own mouth abundant assurance of his restoration by the threefold charge to feed the sheep and lambs, we do not find him again in the forefront. So wait upon the Lord for that restoring word.
Therefore, let us ask in Jesus name, John 14:13-14, thanking Him in advance, Mark 11:24, Heb 11:6, that He would grant to you, to her, to him, and to all of you, the faith and patience that you might inherit the promises, Heb 6:12, the promises that are Yes and Amen in Jesus, 2 Cor 1:20. May the Father deal with you according to His riches in glory by Christ Jesus, and may He keep you in perfect peace as your mind is stayed upon Him. May He guard your son, draw each heart to Himself, and make your home, whether together or apart as Providence orders, a place where Christ is honored, where holiness is pursued, where prayer and the Word dwell richly, and where the joy of the Lord is your strength.
And let us magnify the Father who spared not His own Son, but freely delivered Him up for us all. Herein is love, not that we loved God, but that He loved us, and sent His Son to be the propitiation for our sins. To Father, Son and Holy Spirit be glory forever and ever. Amen.