I am so very sorry 😞 I have been right where you are except she was a 120lb Dobie named Jenna. To this day I cry for her, I get sad when I see other Dobies. Our son was 12 months old and she went at him 2x's and the last chance was a snarl. She never did bite but the threat was real. Unlike you and your boy, Jenna had aggression issues from a year old. She came after me and almost killed my Miniature Schnauzer who was 15 and blind. We tried everything from day one having her in all of the puppy classes, obedience, socialized her with everything people, stores, kids, dogs. When the first episode happened we took her to the vet and she was put on meds. We immediately found a trainer specifically for aggressive dogs and the worst cases. After all that failed and she growled at our son we found a rescue for aggressive Dobes and drove her 6 hours to get her there crying the whole way only to have to go back the following day and get her. The rescuer said she had gotten away from her in the dead dark of night and Jenn ran full throttle head first into an apple tree. She was so scared. I feel terrible still...so full of guilt. 99.99% she was an angel. We, I loved her so damn much. We tried again with her but we were all traumatized by then. I was having a session with my son as taught by the trainer. My son was just sitting playing, not even paying any attention to Jenna. I too was just sitting on the floor with the both of them. Out of no where, she turned towards him and showed all of her teeth. Right away she knew she screwed up and went and got in her crate. My husband and I decided that night that there was only one option and I know it was for the best for all of us, Jenn included. That doesn't make it hurt any less, you are right. The next day my husband took her and had her euthanized. And that too was traumatic because she needed 2 shots. I am bawling as I type this. This was in 2003. You are going to have a broken heart for some time if not forever. Have you considered asking if you can visit him from time to time with his new family? I often wonder how breeders hearts don't shred to pieces when they retire and rehome their dogs. But they do it for the love of their dog. And you are too. What is best for him is what you are doing. Even though it doesn't feel like it. Dogs are not completely happy in an unharmonious home. One thing I did think of is how your daughter kissed him on top of the head both times. A dog putting his/her head higher or above another dog is a sign of dominance. And if he doesn't fully understand that he's not second in charge behind you, he may have been asserting his dominance over her.
I apologize that this is so long. Please keep us updated and I really hope that the best situation appears for you and your boy. Just know that you are not alone...good luck.