Hmm, no-one has mentioned pouchitis, so I guess I will!
Are your BMs normal? Any crampy pains in the abdomen?
Aching muscles, low-grade fever and a general "under the weather" feeling are the way pouchitis manifests for me (I only get mild pouchitis).
These symptoms are usually accompanied by extra/more-watery BMs (hard to tell sometimes what is pouchitis and what is something I ate that was too fibrous until it continues for a couple of days), maybe with an odd colour and smell.
I also get mild crampy pains in the upper abdomen.
Sometimes I only get the muscle aches and fever, which is why I'm chiming in.
Hope you feel better soon.
Sarah in Australia