Hi Joanna,
I have been in a similar situation to yours... My son is now 7 and healthy and above average at school... but when he was a baby he was very behind developmentally - couldn't suck well nor hold up his head as a newborn, did not crawl until he was near 11 months old, couldn't even babble past the age of 1 and a half. I had to do physio many times a day as well as use advice from occupational and speech therapists. The paediatrician told me that they were pretty sure he had autism and were waiting until he was 2 years old before giving a formal diagnosis. A neighbour asked to take him to church when he was around three and a half months shy of turning 2 years old (December 18th 2005), and although his father and I were not believers we thought it would be good for him to go - he could only say 'uungh' and point to things, and still could not even babble 'mamamama', 'dadadadadadad' or anything else. Later that day he was returned home by the neighbour - but something had happened although we couldn't pick up on it... I restrained myself for around an hour before I literally ran to our neighbours house and begged to come to church and know God (it was like I just HAD to, even though only hours before Alan and I had talked about the Bible being a 2000 year old outdated book!!!). In hindsight, God's glory was just all over our son (his name is Josua btw) and caused such faith to rise in us that we couldn't explain our sudden change of heart - and my partner was as affected by this as I was and went to the neighbour on my return home.
Three days later Joshua said 'Mama' for the first time. I ran to my neighbour (she was actually the Pastor of the church) and told her that Josh had spoke for the very first time... 'I knew he would start talking soon' she said. I asked her why she thought that, and she told me that the church had come together and prayed for my son that first day at church, and that he was healed and couldn't have autism (or hyptotonia, nor the suspected epilepsy either). The symptoms of autism, epilepsy and hypotonia stopped over a short period of time, which with Joshua was 'spacing out' and we couldn't get him to 'snap out of it' even if we yelled his name, him constantly banging his head on the walls over and over and over - even while watching TV, his inability to speak and communicate, his extreme oversensitivity - he would cry if he walked on the grass behind our house for 6 weeks because it simply was too much sensory stimulation... plus more of course.
So I pray that your son is healed, that his symptoms start to abate and that he will be a testimony to others of the healing power of the Lord and His love for each of us.
I was also separated on and off from their dad over many years, and we were not together for almost all of 2010 - I was injured and couldn't care for myself, my two older children or my infant son (at the time he was only a few months old). Things had been really BAD, and I was fooled into thinking the only thing I could do was break up with him once and for all, and he felt the same way. I had to abandon nearly all my possessions apart from our beds, clothes, kids toys, photos and a few sentimental things, and move in with my parents. Near the end of 2010 the Lord spoke to my heart and told me that His will was that we be a family and that He had joined us together and blessed us with children - to pray in faith and trust Him to bring our family back together again, that Alan and I would be married, and to trust that He will heal it and our family will live happily in the future.
Alan had a girlfriend and we had not spoken for months - it was very bleak. However as it became the most dire situation and it was at its darkest of moments, the Lord turned it around... the girl showed herself for what she sadly was (angry, violent, wanting his money and as a distraction from the enemy to stop him and I reconciling) and we reunited.
Although things are not going well at present with us, we have just had our fourth child almost two weeks ago and have not broken up since reuniting. We have been surviving some of the most stressful events that people can experience - one after the other, and some are yet to be overcome. However we decided we are in this for life, no matter what. We need prayer ourselves (might put up a prayer request about it

).
I pray that what He has done for us (and is continuing to do as He wouldn't have gotten us together again just for everything to be negative, and He promises to perform our 'good work' until the day of Jesus Christ), He will do for you - that you and your partner are reunited by the speed of the Spirit, that his love and attraction is only for you, that this other woman will gently move on to the person who she is meant to become one flesh with without anyone being hurt in any way. I also pray that this Christmas he is thinking of you and your son, that he is missing you both and that he knows that he should go home. I pray that his heart is softened to the promptings of the Holy Spirit to return home, to leave the other woman, to return to God, to repent of his sin and turn away from it forever. I pray that you are strengthened during this trial of faith, that you are receiving signs that the Lord is working in this situation and that you are at peace knowing that all things are working together for your good, for your partners good, for your son's good and for the good of your family unit. I pray that the devil has no power any longer over your partner and that the devil is not allowed in your life, or your son and partner's lives... I pray your family is headed by angels who are ministering to all of your needs, and that your reconciliation will be like mine - a testimony to the love of God, His greatness and mercy, and to His power to do the miraculous today as He did in Old Testament times. I pray that your partner returns home soon and that you both get married to each other - in the name of Yeshua - AMEN!!!