I don't see any real reason to believe that this snake has a calcium deficiency. What are you feeding it?

You said it's behavior is normal, so the only symptoms are cracked scales and a cracking sound when handling the tail; correct? Is the tail held abnormally? Painfull reaction when touched? Snakes in pain often go off food, and/or act abnormally defensive.
The sound/cracking that you heard could have been, as you described, breaking bones, but unlikely. FYI, it would be the lateral processes of the vertebrae as there are no ribs caudal to the vent. There are other possibilites, but the most common that I can think of would be a simple case of vertebral re-alignment. Kind of like when a chiropracter adjusts your neck, or you crack your knuckles. Some snakes seem to exhibit this phenomenom more often(arthritis?).

If your snake shows signs of pain, or other symptoms, then consider a vet visit for proper diagnostics. If the skin condition worries you, a vet will also likely be able to help. It could be anything from a bacterial/fungal infection, to dehydration, malnutrition, or more discreat problems like hormonal imbalances. A good rule of thumb is to see a vet's advice if it has not greatly improved after the next shed.

Good luck and take care,

Ian

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