Hi gumby44,
I would definitely have your vitamin D level checked. After finding out I was low, I also began taking it regularly (I now take 2000 IUs per day as my Dr. recommends). It seemed to help a little with the body aches, but I definitely still get them---kind of like what you described, with the overall achiness feeling sort of like the flu, and usually worse in the afternoons and evening.
Curiously, when I mentioned my overall body aches to my fantastic GI doc, he said he hadn't heard of that being related to Crohn's. (He's heard of the joint aches though). So I'm still puzzled as to what my achiness is caused from.
I'm very curious as to what you find out!
Oh, and although your vitamin d level might technically fall into the "normal range" on your lab results slip, a "sufficient" level is at least 30. And according to my primary care doc, at least 40 is ideal for preventing osteoporosis.