Both my daughters were diagnosed with spondyloarthropathy. The diagnosis has been changed to Ankylosing Spondylitis for both as the disease progressed.
They both have a lot of joint pain - sacroiliac joints (in the lower back), hips, knees, ribs, heels and stiffness. The pain increases when they aren't active so they both have trouble sitting for a long period of time and sleeping.
For this kind of juvenile arthritis, NSAIDs, methotrexate and biologics are used. Most kids with IBD are not supposed to take NSAID (like Advil) but my younger daughter's GI allowed it because it really helps her joint pain (she takes Mobic, a prescription NSAID). If NSAIDs don't work, rheumatologists either add Methotrexate (sometimes they try Sulfasalazine, but our rheumatologist said she doesn't think it works well) and then they go to biologics. The ones approved for this kind of arthritis are Enbrel, Remicade and Humira. I think Cimzia is also sometimes used but I'm not sure about that.
Since M (my younger daughter) has Crohn's she has to be on Remicade or Humira, I assume it would be the same for your daughter. Both my girls have been on all 3, my older daughter is finally doing well on Humira (+methotrexate) and my younger one is on Remicade (and not doing so well right now).
Only my younger daughter has Crohn's and she hasn't had it very long, but it seems like her joints can hurt when her stomach is fine and vice-versa, so I don't think they necessarily flare at the same time.
If you do try an NSAID for Grace (your GI would have to approve it I assume), just remember that it's common to go through a couple before you find one that works well. There are lots, and my older daughter has been through at least half of them, before settling on Naproxen.
I know for other kinds of juvenile arthritis there are different treatments but I' not really familiar with them. I also don't know if the treatment would be different since your daughter is so young.
Hope this helps and Grace starts feeling better soon!