back molars are bigger teeth ( ha obviously ) so they leave a bigger hole , which can take longer to heal
It can take up to a week for the pain to stop, if its excruciating however, I would give your dentist a call , just to make sure they got everything out .
You say you should have had root canal done, but in all honesty , root canals are only 80 % effective, and don't always work long term, most dentists will suggest a RT first, so the fact they took them out , suggests they knew there wasn't much they could do to help it .
(Ive been a dental assistant for the last 5 years btw, however I think Lady lizard is a dentist, so she would be able to suggest a lot more reasons why they may still be hurting than I can )