Did you ever get new x-rays of his teeth? In the x-rays you got a few months ago, could you tell if his roots or teeth were elongated (if you can find a way to post them people can tell you if they think they look elongated)?
Watering of the eyes is a sign of root elongation, but since he was getting better it may have been something totally different. Maybe he got an eye infection that spread? I have no idea but from what you are saying he seems to be having pain while eating. Him eating a lot is a good sign, though and with that you know his pain isn't bad enough to deter him to eat.
Do you have a scale to weigh him and if so has he lost anything?
Also, do you know if all the abscesses cleared up?
Good luck, I hope he makes it again.