I was also found to be vitamin d deficient last year, and was put on a super dose for a few months. Because it did help my pain a bit I was allowed by an endocrinologist to stay on what is considered a high dose (though not the super high I was on at first) and I still come back at normal levels in blood tests.
I do take calcium with it, but the important point that occurred reading your post, yosafbridge, is that I also take a magnesium supplement that balances the calcium I take (a ratio 2:1 of calcium to magnesium) which O believe stops, or reduces anyway, the muscle pain.
Admittedly I also have fibromyalgia syndrome, which is known to be associated with low magnesium, so it's obviously something my body probably needs, but magnesium is commonly known to be a muscle relaxant.
I actually also take zinc. I read somewhere that if you're taking vitamin d, you also need to take calcium, magnesium and zinc, and preferably vitamin k and something I else I can't remember, though I don't take the last two.
OK, just checked for the link for the thing I read - it's boron that's listed, as well as vitamin A, though the latter is dangerous in overdose so I'd only take that under medical supervision.
I don't think I'm allowed to give the link in my post, but if you google vitamin d cofactors and the vitamin d council I'm sure you'll find it. Feel free to message me if you can't.
HMS (diagnosed 13/9/12 confirmed at UCHL 27/11/12), ME, FMS, autoimmune hypothyroidism
"The trouble with having an open mind, of course, is that people will insist on coming along and trying to put things in it." (Terry Pratchett)