I have a 12-year-old daughter too, and EEN was helpful to her earlier this year. She got Peptamen 1.5 via NG tube for 10 weeks, and she's now getting supplemental EN via tube three nights a week.
We were trying to use EEN to induce remission while we gave Remicade a change to kick in. For many kids, that works, but in E's case, the EEN was not enough. She ended up in the hospital with an abdominal infection two weeks into EEN. She got IV antibiotics and steroids in the hospital, and then started budesonide and methotrexate (in addition to the Remicade and EEN) when she went home. With all that, she's finally getting better.
So that's a long way of saying that EEN alone wasn't enough for my daughter. However, it did keep her off prednisone, and I believe it gave her body the nutrients it needed to start healing. She's also gained more than 20 much needed pounds since January thanks to the EN.
I understand completely your desire to taper your daughter's prednisone, but are you considering any maintenance meds? EEN is not a long-term solution, and once food is reintroduced, inflammation usually returns if you haven't started a maintenance medicine.
Edited to add: I just reread your original post, and saw that your daughter started 6-MP and budesonide recently. Will she stay on those, or does your doctor think they have anything to do with the stomach issues?
Good luck with the EEN, and I hope that your daughter is feeling much better soon.