I used to get similar kind of pain just before my first surgery. Specially in the elbows , everytime I woke up or in middle of night. It was stabbing pain. I never found out the real cause as I was running on very high doses of steroids prior to my surgery . But my GI called it as a sign of low calcium density in bones which was affecting their strength to hold the body. 

Notice that if you'll get the pain in the side on which you've been sleeping. The part of my body which was in contact with the bed  it pained the most. 

Are you still taking any steroids ? Cause they tend to weaken bones. Or a having deficiency of calcium in bones ? Or arthritis is a cause ?

After surgery I took calcium supps, Vitamin D3 supps and started exercising regularly though I know I still have a very low bone mass.

HI Taylor, Yes that it is exactly like me. I think joint pain goes with the territory of bowel disease of many of us. I have migrating, inflammatory arthritis in the large joints like you, it only commenced for me 10+ yrs post colectomy. Mine was so bad I could barely get dressed or walk up stairs. So I had a course of prednisone at first, then was put on humira. This seems to have controlled it for 1.5yrs. But I am now trying to go off it. I haven't had it for 2 months now and I am doing ok. I would speak with a gastroenterologist or rheumatologist - I do both. 

Hi Taylor, I have pretty bad inflammatory arthritis. Auto Immune conditions often work in families Colitis/Arthritis/Psoriasis. I had my pouch for 24 yrs before I had any joint pain but once it started out just progressively got worse over the years. It effects my right Sacro Iliac joint, right hip and left knee. I highly recommend you go see a rheumatologist, I regret not seeing one earlier. Im now on Humira and Methotrexate to manage the inflammation. 

I was diagnosed with Enteropathic Arthritis in Spring 2017.  I had an acute flare with major swelling in my left knee.  I am on Sulfasalazine which keeps the major swelling events in check but I do have chronic pain in multiple limb joints and SI joints that comes and goes.

I've had my pouch about 14 years and I have arthritis that used to give me terrible pain. Rheumatology Dr put it down to post colitis/bowel related issues as a strong factor. Had radioactive injection for my knee and I get steroid injections in my wrist. Sometimes it's lack of vitamins that causes the joint pain (coupled with stress)
Good luck!