Another thought would be to try goat milk. I know it sounds strange, but it's worth a shot. For some reason, my system doesn't tolerate cows milk really well, but does handle goats milk and goat cheese and goat yogurt just fine. I don't know why, but my guess is that it has to something to do with different enzymes and proteins but I don't really know for sure. All I know is that it works.
Redwood Hills Farm produces both milk and yugurt (I believe the farm is in Oregon)...the only drawback is that the milk only comes in whole and 2%, not nonfat, and it's really pricey, but it might be an alternative in the short term.
The milk is available at some QFC's, Trader Joe's, Whole Foods and PCC, and I think the yogurt is available everywhere but QFC.
You may want to try a good multi vitamin as Marda suggested, but as she also pointed out, your little one really isn't feelng well, so don't stress too much about the calcium right now. Chances are that thing will right themselves when she's feeling better.
Hang in there. I hope your little one feels better soon!