Usually with Iron / Vitamin B12 deficiency there is extreme fatigue and weakness, not muscle pain. They may have the same symptoms, however, there is a difference between iron and vitamin B12 deficiencies and they are medically treated totally differently. Nothing should be 'assumed' without lab results. You should have your MD do an iron profile blood work to determine if you have any type of anemia. If you do, this will indicate which one and you can be treated properly. If you have muscle pain, they should also look at your potassium levels. Once you are diagnosed and treated, if it is an deficiency of a nutrient, then the pain eventually will go away. Suggest you eat healthy food by consuming all the food groups daily.
I suffer from Vit B12 deficiecy due to malabsorbtion syndrome caused by loss of 99cm of small intestine from a MVV. I take monthly injections to keep my level normal. When my level falls below normal I do expereince some muscle pain. However recently my Vit D level was found to be extremely low and I had much more muscle pain and aching than I do when the B12 becomes low. Both can cause depression so if you are feeling a bit "blue" or have lack of energy this can also be caused by low levels of B12 and Vit D. Yes, they will resolve when your levels return to normal which if treated correctly can be fairly soon. Please feel free to ask my any other questions you may have. I hope you're soon feeling much better. Take Care, Tuck