I no longer have an ileostomy, but I did have one for over 2. 5 years so I am very familiar with the pluses and minuses of having one. Recovery from my first surgery was very slow as I had ileus, obstruction, and swelling. My output was initially also very thick (likely due to the prolonged ileus). Like you, I was also very aware of peristalsis and could see my stomach move around the stoma (I still feel things around the old stoma site even now years later, though I have confirmed adhesions and they are the likely culprit). If blockage, infection or stricture have been ruled out in your case, this seems like par for the course. Swelling after this kind of surgery is normal, and it is not uncommon for the stoma to shrink even to half the size it was post op in the first 8-12 weeks after surgery. You may have to adjust your ostomy system accordingly as the stoma continues to shrink down. The good thing, as others have mentioned, is that you do have motility and you are passing stool, so an obstruction is less likely. The pain you are feeling may be due to residual swelling or pain at the surgical site, but if it persists, you should get rechecked just to make sure there isn't something else going on, for example, stricture, infected suture, etc.
One final thing, what is your diet like? This early on after getting an ileostomy, you should still be following a low residue diet. It's not recommended to have foods with a lot of roughage; these have to be added back into your diet gradually, usually after the first 8-12 weeks when most of the swelling has typically subsided. If everything else checks out, and you have not yet modified your diet, that could be some of the cause for your pain. Google "low residue diet" and try following that for a few days to see if things improve.
Best of luck!