I happen to have first hand experience in this as I am one who fought the war on tooth decay in the US Air Force serving as a dental technician 1st class (uneducated enlisted position).
You didn't say in your post but I'm assuming it was an upper tooth since you mentioned having to go back and forth for x-rays as the roots kept breaking off. If it were a lower they would just keep digging with the 301 elevator until they cleaned it out good. The problem with roots breaking off in top teeth is the danger of pushing them up into the sinus cavity which can be a big problem requiring immediate surgery where they cut the perimeter of the palate and drop it down to access the sinus cavity to remove the root tip.
I'm not saying they left a tip behind but if they did it is major malpractice as an infection could result and this might be why he is feeling bad?
I would go by the clinic and ask them for a copy of the x-ray showing him to be free of root tips.
Don't worry over the mercury part of the extraction as the mercury in the Amalgam is chemically locked and harmless even if swallowed it would just pass without harm. The danger from Amalgams is the constant chewing and grinding which releases cumulative amounts over many years. I had my Amalgams drilled out three months ago by a regular dentist not using any precautions as preached here on the zone as I know better than to let unfounded fear separate me from my money by going to some holistic quack that caters to the fear of fools for extra $$$.