The calcified canal has nothing to do with your arthritis.Have the denture checked for any irritation that it might be causing.
Some teeth over time tend to calcify inside so it can be very difficult to access the root canals. This probably isn't related to your arthritis but more a factor of age, fillings placed on a tooth, exposure to hot and cold stimuli over time, grinding issues, etc.. It's quite a common problem that dentists encounter.
It's unusual to have gums that are still very sore after two weeks. It can be due to a problem with your plate or the root canal. Is your denture impinging on the area? You might want to contact your dentist for an appointment to find out what is going on, and if it is the denture to have it adjusted.
If the gums are still sore at the extraction site, you could have a mild, persisting infection or residual sharp socket crests impinging on the gum. Again, it's best to have it checked out since two weeks is quite a long time.