Hi Dean. The normal exams, blood tests and CT scan are very reassuring. The symptoms you are having may actually be a good sign, as the nerves that have been deprived of B12 (and damaged as a result) are now recovering and reparing themselves. This often results in intermittent, sporadic firing that creates abnormal sensation without actually representing any pathology. Recovery can take 3-6 months as nerves regenerate rather slowly. If you are working closely with your family doctor or a neurologist you should not be concerned about it being something else. They should be monitoring you for other possible conditions.
This could be part of the recovery process of the neuromuscular units affected by the B12 defiicency, or it could represent strain from increased activity now that you are getting better. This would be especially true if you recently took up a regular exercise program, are weight lifting, or doing more of some activity around the house such as going up and down stairs. Either way, monitor this deep ache and let your doctor know if it progresses. As for supplements, the only would you might need would be a multivitamin. This would certainly be the case if recent blood tests indicated that your sodium and potassium levels were within the normal range. You could also have your GP check your calcium, magnesium and phosphorous levels just to be sure.