TJ's Mom - Geez. My daughter is 9 and was just diagnosed with Crohn's within this past year. I can't imagine how frightening it would be if she were EVEN younger. I feel for you, I really do.
Anyway, my daughter had a lot of fevers too, before we knew what was going on. Almost nightly, and sometimes so bad that she would get the shivers/shakes and cry. Her first course of treatment was prednisone and pentasa. She got better quickly, but flared up after about 10 weeks of stopping the prednison. She is now on pentasa and entecort and is doing what I would call "decent." Thinner than I would like, but seemingly okay.
I recently started giving her Ensure Plus again...as a dietary supplement to help boost/maintain her weight. For some reason, she is feeling better since we started that. She only drinks about 1/2 bottle nightly. Have you tried that for your son? Many here say the vanilla is the best flavor. My daughter has been drinking the milk chocolate.
You may also want to look into an enteral nutrition formula. I have not ordered it for my daughter but know someone who's child has had great success with it very recently. It's called EO28 Splash. I don't know the website name, but google it and you will find it easily.
Also, do you have your son on probiotics? If not, you might want to consider that as well. They are said to help boost the immune system by fighting off the unwelcome bacteria in one's body to replace it with the good bacteria. There are many many brands of probiotics on the market. (My daughter takes an Align capsule daily. If your child won't swallow them, open it and mix it into some juice with a child's medicine dropper, then squirt it into his mouth. Works like a charm here and Welch's grape juice hides many evil flavors.)
Hope this was helpful.