If there is gut damage due to an allergy or intolerance, the effect can be cumulative. The only way would be to completely eliminate the offending food and allow 2 weeks to get it out of mother's system and milk, then another 2 for it to completely clear baby's system. So if the gut is getting more damage, that can lead to tummy-aches and pain he can't filter out unless he's exhausted and not even then, along with eczema that's already there. Not saying this IS the case, just that one can't really rule it out.
Meanwhile, I forget if I suggested massage while winding down, but if I didn't I am now. LOL With Josie, we had to keep her first A time extremely low-key for a while and then we just wound her down in her room and put her in bed when she was very drowsy. This also gave us the chance to really get more familiar with her tired cues. She was much younger at the time, though, more like 3 months, but a similar strategy might hold true.
Something else I remember doing with her when she was a bit older and was waking crazy early in the mornings and I just couldn't get up and be awake was to go to her room the moment she started making noise and just sit with her with the idea of holding her to sleep before she was really awake: her room was still dark, and I mostly wanted just another 45 minutes of sleep myself, and we'd often fall asleep together in the chair beside her bed. One morning she started sleeping through! (And then a couple weeks later we were literally going to be late for an appointment so had to wake her at 8:30AM and that was the end of it, but by then she'd re-set somewhat, so at least no more 6AM wakings all the time.)