Jay79, I think you're on the right track when thinking about
your ankle. I'd also want to talk to the ortho about
whether another surgery to take out the hardware would add insult to injury.
For many years joint pain was my main complaint with regard to my IBD. Every time my joints started hurting in a flare they would begin at old injury sites. I think there's some kind of scar tissue in there (even at the soft tissue injury sites) that gets targeted by inflammatory response somehow.
I found it very helpful to bring a rheumatologist into my care team. He was really the one that took the most thorough history and did a really bang-up job of eliminating possible issues and getting my GI to focus on resolving my active IBD to relieve the joint pain.