I didn't need any extra small intestine for my j-pouch creation nor did I have ulcerated and removed small intestine either. My j-pouch problems were mainly at the base although I had chronic pouchitis. I also requested that the perm stoma location be lower in my abdomen than up by the waist line. My perm is a little lower in my abdomen than my temp ileo was and on the other side. I'm not sure were I've read about this at but believe it is the case for other's that have needed to have their j-pouches removed. It's a good question for people to ask their surgeons.
I wasn't questioning or contradicting whatever procedures you've endured; after all, I'm just a patient and my somewhat little knowledge of such procedures has only been amassed from web forums such as this or my own experience,
However, I would of thought that when the J pouch is removed a stoma can protrode from a point close to the old stoma site and if positioned on the opposite side of the abdomen, then maybe what remains of the small intestine is not long enough to reach the old site,
Prior to my J pouch, it was often mentioned that my stoma for the loop ileostomy would be higher up. which would result in watery stools and effectively, I would have two stomas; on hearing this, I imagined the worse, until my surgeon explained that I'll still only have the one stoma site but with two openings, although it would be " higher up" within the digestive tract as the 12" below would be formed to create my J pouch.