Your heart has been poured out before the Lord and He has heard the cry of a mother who loves her children and loves her Savior. To be aligned is not to arrange circumstances to our liking, but to be brought into simple submission to God, to surrender every proud pretension and to be made teachable before His good pleasure.
It is right to pray, as you have, to be made simple, teachable and mild, awed into a little child, pleased with all the Lord provides, weaned from all the world besides. This is true alignment, to say with a complete surrender, Father, not as I will, but as Thou wilt, and to surrender yourself also to His method of operating upon you. You ask that God would honor Himself in you and in your son and daughter, and that is the prayer He delights to answer, though He may answer it not as we expect, but as His wisdom appoints. No father can let his child bend his little fist in defiance and yet treat that child with the same nearness as those who submit themselves to him, and so the Lord calls us to bow the heart to His fatherly rule and to trust His hand even when the way is painful.
You feel as the father of the prodigal felt, watching a loved one go into a far country. Remember how that father acted. He had a long range of eyesight and saw his son while yet a great way off. He did not note him as a stranger might, but as a father alone can do, with a quick eye of love. And when the prodigal returned, overwhelmed by his past life and ready to say make me as one of thy hired servants, the father stopped him with a kiss, and with kisses again and again. Those repeated kisses meant full restoration. Before the family fellowship, before the music and dancing, before the servants had prepared the meal, his father kissed him, and by that kiss his sonship was acknowledged. He was to his father as if he had never gone away. So it is with our God. When a wanderer returns, there is joy, there is music and dancing, and they begin to be merry. He presses the returning child to His bosom and confesses him once for all as His own, the kiss being the seal of forgiveness.
Take comfort also from Peter. His fall was soon over, like a little child learning to walk, scarcely down before his mother has him up again. His restoration was brought about by a look from the Lord, a look which severed him from the crowd and broke his heart, and by the Lord's having prayed for him in private. That same Lord still looks and still prays for His own. And sometimes the very falling and wandering of a child is blessed of God to make him more careful in the future, that he may be a better man afterwards. It is good for a man that he bear the yoke in his youth, and discipline learned under a father's roof, if it be in Christ, may be the Lord's own schooling.
Therefore we will pray with you, not that God would merely fulfill our desires as we frame them, but that He would do what is truly best for your son and for you. We thank God that your son is finding a place in a church and in a school where he may hear the Word, and we pray that the Lord would make that time fruitful for his growth in Christ and in true manhood. We pray also for his father, that if his walk was shattered years ago, the Lord would restore him and make him the man he ought to be, that he may train his son not in his own strength but in the fear of the Lord. Whether the Lord in His providence brings your son home to dwell again under your roof, or whether He plants him for a season where he now is, our prayer is that your son would be the Lord's wherever he is, and that you would be given grace to be pleased with all the Lord provides, trusting that He who sees from afar will keep His own.
And we will not forget your daughter. You have done well to remember her. We pray that the Lord who seeks the lost piece of money till He finds it, because it is His own and He values it, would seek her heart and align it with His Word. Pray that she too may be brought to know herself as His child, to claim her privilege as a child and to live as a child should. Build her up daily by the Word, by prayer, by your own example of quiet submission and holy love, that if and when the Lord reunites you all under one roof again, it may be to share one Christlike love.
May the Lord make you steadfast in this trial. Do not hurry from one thought to another to silence conscience or sorrow, but sit still under His hand. He can make what seems like the end to be a new beginning. He rejoices over a poor soul that has wandered far but at last returns, and the poor soul shall be happy too. Continue to look to Christ alone for salvation for yourself and for your children, for there is no other name by which we must be saved. Cast your burden upon Him, surrender your will to His, and rest in this, that everything He does is in your best interest, even when you cannot see it.
We pray that the Lord will align you, your son and your daughter to Himself, that you may be kept in His love, restored where restoration is needed, and made to rejoice together in His mercy, whether together in this life under one roof or together forever in His house above.