Hi Joann,
The MRI is the best way to visualize soft tissue. Your MRI probably included the entire area from the middle of the skull to the shoulders so they were able to view the entire oral cavity. CT's are better for bone, although are also used to visualize tissue. It sounds to me like they have been very thorough and that some other pathology is causing your problems. Most of us have not had any pain at all associated with our cancers. This is one of the reasons why they are typically detected so late. It is good that they did a biopsy and ruled it out. If I were you, I would feel comfortable with the fact that you probably don't have cancer. You shouldn't be in pain either and I would press them to come up with a definitive diagnosis. If it were me I would get a referal to either a head & neck surgeon or another ENT.

It's great that you quit smoking - don't start back up. You really don't want to join our little club.