This is going to be very non specific, but my wife's cousin had been out of Thailand for over 30 years, although he was a Thai citizen by birth.
Passport was long expired, it was last given when he was a child. never got an id card. Mother and Father long deceased. Came back for a new life, not a US citizen.
Long story slightly shorter. The next thing to do was to get his family history from the Amphur and have witnesses say that he was born there and that they remember him etc. That took a month or two to get that situated out.
Unfortunately the Amphur decided that the ID card, that he needed to get a drivers license and a new passport and healthcare was "delayed" I think this was 6-7 months until he paid the tea money for it to magically appear.
This was 4 years ago, everything is fine now.
Your son had a Thai passport already, so that may smooth things over a bit. You may have to get a family history from the Amphur you were born in, unless you already have one. Wifes birth certificate, marriage certificate and any divorce papers from either one of you will need to be certified and translated. They will possibly need bank statements?
It would possibly behoove you to get an english speaking Thai lawyer to help out, this is a bit of an unusual case, my wifes cousin was the closest thing I could think of.
Good luck.