There can be a lot of different reasons for the pain, especially since it goes away once you intubate.
1. Pouchitis can cause irritation of the pouch lining and can be relieved through a treatment of antibiotics.
2. Food allergies or sensibilities. Either get tested or try an elimination diet. By keeping a food diary and doing the elimination diet: you do a 24 liquid fast (only water, tea, juices etc) then introduce 1 food at a time, 1 day at a time (I always start with chicken the first day, it is rather pouch-friendly) and then introduce 1 protien per day at a time (you can accumulate them), then vegetables, fruits, nuts or nut butters and seeds and finally carbs (breads, pasta, rice, beans...). Keep the diary going and write how your body/pouch reacted to each new food and do not forget to try them first Alone before mixing the food with another (write down that too. ex. sandwich or chicken & rice...). Do not forget to write what you drank with the food and how much.
You will end up with a very percise list of the foods that are pouch friendly for you and work well together.
3. A pouch twist or the pouch has fallen off of the wall. NO one thinks about this one but it happens more often than you can imagine. I am a bad healer and once my sutures have 'reabsorbed' my pouch just 'collapses' off of the wall. I needed permanent sutures to hold it in place (this is rare but...)Sometimes only part of the pouch is healed or scarred onto the abdomen and it 'partially sinks' and I get a twist. Either way, as soon as it starts to fill it hurts (that is my hint)because it pressesd on things that it shouldn't (bladder, uterus, ovaries. Whatever is in the area at the time). It is very hard to catch this one. You cannot tell in the typical contrast studies because you are laying down on a table! You have got to convince the radiologist to do the study with you 1. on you back. 2. On your right side. 3. on your left side. 4. Standing up!!!!!
It is the only way that they can tell if it is twisted (at the neck of the valve usually which can cause problems intubating too and sometimes leakage when full).
My radiolist acted as if I was a nut case when I asked him to do it that way. Then he finally agreed (I can be very persuasive) and he was shocked. My pouch was litterally hanging sideways. NO wonder I was having problems.
4. A hernia. Sometimes they hide behind the pouch or near the stoma and can be small but painfull when the pouch fills up and pulls down on the abdomen. (sometime they are the result of a twist or cause it...I ended up with my pouch getting 'stuck' inside the hernia and had to have ER surgery to get it out!)
So, those are just some of the possibilities. My first step would be the diet and to have your surgeon book a contrast study (you are awake, it is painless and they drip a contrast fluid into your pouch to visualise the valve first then the whole pouch.)
Once you have that done you will have a better idea of what it is or is not.
Hope that this helps