Apical periodontitis. how to treat it.

I have constant jaw pain under ear and neck for 15 months now. Have tapping and biting pressure on tooth 46.had root canal and crown. Still no changes. Same pain for Biting pressure on it. It hurts in the tooth and gum even if pressed with fingers. I have neck pain and have small lump for more than an year. Had CT scan&normal. I have jaw clicking and grating sound. Taken MRI,CT of jaw. Normal. They said it's Myofascial pain and doing physical therapy for it. Biting on this tooth on qtip hurts in the lower jaw under ear lobe. I am not chewing on it or using that side at all for eating. Using only the opposite side. I went for another Endodontist opinion. He took x-rays and said tooth 46 has apical periodontitis. Not sure if it's been present since beginning of this pain episode. He put me on antibiotics to see if it helps. Tooth 47 hurts little when he put bite stick to bite on. He said I have PDL widening on it. How to treat apical periodontitis? retreat RCT or extract?