Hi J.,
As a parent, changes to sleep patterns are concerning because of what they could represent. I know many allergy and digestive problems are first seen in sleep disruption. If I had it to do it over again, I would certainly try some things to see if you can impact it which would give a direction. The first thing I would do is remove milk either all together or anytime past about 3-4:00pm. Change to rice milk if you have to or just do water or watered down juice. Also, you can add a proibotic to her juice (that you can get at whole foods or other natural food store). The reason for this is to see if she is having digestive issues or yeast overgrowth (both which cause sleep disturbance). If these seem to have an impact, you can start your research into how you could impact those using natural medicine, etc to correct it.
If she was vaccinated in the last 2-3 months, I would certainly find out what vaccine she had and read on that one to ensure she is not having other symptoms you are missing in relation to that. There are several great vaccine books out (Stephanie Cave and Marhon have both written good books you can find on Amazon). There is also a DVD out that I hear is very informative.
Best of luck and I hope happy return to sleeping! J.