When you go to the ER with vomiting after you have had abdominal surgery, they are looking for a small bowel obstruction, not pouchitis, and that is the correct thing to do. It is correct, because small bowel obstruction can be an emergency, while pouchitis usually is not. X-rays and CT scans will not show much of anything unless you have a complete obstruction. Partial obstructions are fairly common, and while they cause a lot of pain, they usually are not serious. But, vomiting can be a sign that you have a complete obstruction (usually at the stoma site), so you were smart to go to the ER and get that ruled out.
Rectal pain following this surgery is fairly typical, but it is a matter of degree as to what is typical and what is something serious (like an abscess). You say your surgeon just puts you on more medication, but what is that medication?
So, from what I am seeing, it appears that you have two separate things going on. You probably have not been released surgically from your surgeon yet, but you can ask him if you can see your GI for other ideas.
The good news is that these things usually work themselves out with time.
Jan