Yeah, the muscle soreness sounds extremely normal: the flu-like feeling, perhaps not so much. Depends on how bad it was.
When I had pancolitis, my exercise tolerance was extremely limited on some days: 5 minutes of playing football with my nephews left me doubled over with dizziness and nausea and I would have to stop. Other days I could go on for longer, but I would always have to stop at some point. Not that anybody knew it, but my Crohn's was actually pretty bad and I was usually anaemic, had regular fevers, etc. I was underweight, unfit and unhealthy.
Dx Crohn's in June 2000. (Yay )
Tried: 5-ASAs, azathioprine, 6MP, Remicade, methotrexate, Humira, diets.
1st surgery 20/2/13 - subtotal colectomy with end ileostomy.
2nd surgery 10/7/15 - ileorectal anastomosis. Stoma reversed and ileum connected to the rectum.
Current status: Chronic flare. Do I have any other kind?
Current meds: 50mg 6MP; Entyvio (started 3/11/16)