Well I've read and re-read through this thread a couple of times now. It's a tough one for sure. I wonder if a professional behaviorist might be helpful? There are so many things we do not to see in text. And what is one thing to some people is interpreted differently to another. Caiques are such a beaky breed their constant rubbing and beak banging can be confusing.
While I do agree with getting a second opinion on a health check up. I think some target training would help deal with daily interactions and basic cage maintenance. No hands no towels. Get yourself a chop stick or a wooden spoon handle, some kind of long stick type object. Does he take food from your hand? Or is he totally afraid?
After all the toweling he most likely doesn't trust you at the moment much. It's almost like you have to hit the reset button. Treat it like a new relationship.
Start from scratch. If he's food motivated I would find the treat he likes most and only use it for training. I've seen target training work wonders with hands off parrots. I've even used it myself when volunteering at a rescue. I always had nut treats in my pocket. The Big Macs and Zons learned I was the bearer of treats. I would target them to one side of their cage and offer a good sized treat then I could change out food dishes or a toy without being lunged at. After a few sessions and some calm talking I could do my work without much worry. Sometimes they would voluntarily move to the usual spot before I targeted. Targeting basically asks the bird to touch an object or move to a particular spot for a treat or positive interaction.
Good Bird Inc (Barbara Heidenreich) is a great positive reinforcement training resource.
Granted in your case it may take a little more time to recover the trust but it can be done.
I think it would also be good to consider your own energy when you're around your bird. It obviously confusing and upsetting to suddenly have issues where there were none for years. Our emotions get the better of us most times. Consider keeping a daily journal about your daily interactions. Note your birds physical behaviors as well as your own. Focus on the details. Every feather movement and eye pin is a communication from your bird.
Keeping your notes specific to facts will help you learn to retread your bird. It would also be helpful to note how you feel. It can be relevant. But avoid labeling what you think the bird feels. We can't know that for sure. We can only know what behavior we see.
There's more I'd like to offer. There's lots to consider. But this is all I have energy for at the moment. Hopefully some will help. Or maybe I've just babbled