You might want to try using a diuretic herbal tea, such as dandelion, juniper (berry),spearmint or peppermint. This may help flush out whatever the MSM is detoxing. I just started taking MSM one month ago, so I am no expert.
Is your urine very yellow or thick? Mine is, even though I am drinking a good amount of water and thyme and spearmint tea.
I also suggest sweating. If you don't feel like exercising with a headache, I suggest a sauna. I ran for the first time in a year or so today, and when I got back, I washed my gear by hand, as always. There was more gook and grime in it than I had ever seen before. I figure it is the detoxing, or, at least, I hope it is. I'm going to continue with the short runs.