Have you considered a second opinion? I ask because increasing the MTX and not the Remicade seems odd to me. Also, supplemental EN will certainly help her gain and grow, but it won't induce remission. I guess now that he's adding Prednisone, it makes more sense.
But I have never even heard of Kate Farms - kids are usually put on Ensure/Pediasure/Boost if they can tolerate polymeric formulas. If they need semi-elemental formulas, it's usually Pediasure Peptide or Peptamen Jr. If they need an even more broken down formula - an elemental formula - then Elecare or Neocate Jr are used.
Have they done her Remicade levels?
Where are you located? The best pediatric GI departments are at Boston Children's, Cincinnati Children's and CHOP. A second set of eyes can REALLY help.