minnie...most of my CD issues are extraintestinal (until this latest flare). I should have known better the flare was coming because my joint pains increased in quantity and severity. I also had some mouth issues and my skin had some funky patches. Like kaz said, the only thing I do to treat the joint pain is try to keep the guts in check. I am sure you know that NSAIDs hurt your guts more so I don't even attempt those.
You can consider a rheumatologist. However, I have found that heating pads, warm showers and gentle stretching exercises to be my best friends (that is after getting my gut in gear).
ps...I don't have a proctitis dx, but I have a lot of perianal issues. I am just using OTC cortisone on those to try to tame then. Wish I could help more on your other question. It sounds like you need to get the inflammation down like they said. Hope you get some reliefe soon