According to what is said here, those who posses the Shikotsumyaku are able to create bones by manipulating
their own skeletal structure (their osteoblasts and osteoclasts). By infusing their calcium with chakra, they could manipulate the growth and properties of their bones to their liking.
From what I can gather (given that I am not an orthopedist, and have no knowledge in this field) osteoclasts and osteoblasts are instrumental in controlling the amount of bone tissue: osteoblasts form bone, osteoclasts resorb bone (meaning they break down bone and release their minerals, which results in a transfer of calcium from bone fluid to the blood).
I think this part would explain how he is able to create bones in itself.
However, after reading the first comment you left in Curtis Sumpter's answer (Fair enough. But the human body just doesn't have enough calcium for his jutsus.), I've tried to understand how calcium is regulated in the human body. I came to the conclusion that parathyroid hormone and calcitonin are the hormones that regulate the calcium levels in the body, the former acting to increase the concentration of calcium in the blood and the latter to decrease it. Perhaps he had some type of deficiency in the way he metabolised calcium, which could have lead to hypercalcaemia. Some of the symptoms seem to match Kimimaro's, namely fatigue, abnormal heart rate, vomiting (he coughed blood, I'm not sure if it counts in the same way...) and he ended up dying of cardiac arrest. If this were the case, the fact that he is able to manipulate osteoclasts and osteoblasts may be a result of his abnormally high levels of calcium in the first place. This could also be the reason for it to be such a rare Kekkei Genkai, even among members of the Kaguya clan. It could be something like a Potential Bloodline or a Genetic Advantage (or disadvantage, since he ended up dying of it, if this speculation is correct).
As far as real-world actual explanations go, with my limited level of knowledge, this is as far as I can go (and still, an orthopedist may look at my explanation and find it a lot of humbug).
On the other hand, the explanation provided in the Wiki also says that, aside from manipulating the osteoclasts and osteoblasts, they infuse their calcium with chakra. So this completely ruins real-world actual explanations, since it introduces a completely different (and actually nonexistent, AFAIK) circulatory system. This means two things: firstly, it introduces a new variable, that potentially renders all of my above possibilities moot; and secondly, that the infusion of chakra into calcium could actually modify its properties somehow (this is actually contained in the first thing, but nevermind...). This last paragraph could actually mean something like: don't overthink it, it's just a cartoon... :D