Concerning GI issues

For the past 18+ months, Gracie has dealt with persistent diarhea, a low-grade fever and the inability to tolerate her feedings.
The fever is an odd thing - - not sure if we can really call it that now as it just seems that she has "regulated" a bit. Up until she was about 3 1/2 yrs, her temperature ran pretty low - - about two and a half degrees below normal. She inexplicably began running just above normal summer '06 and it never went back. Her "new" baseline temp used to be a fever for her. Several of her doctors had previously told us that her abnormally functioning hypothalamus (which regulates your body temperature) would not ever change. She has had lab after lab ordered and nothing explains the cause... it's been "written off" by mostly everyone as her "new baseline temp", but it seems to me an odd coincidence that it occurred at the same time her bowel issues increased.
She has had persistent recurrent diarhea pretty much since August 2006... and it has only improved slightly while on one med. No results in labs explain the problem... none of her regular medications explain the problem and her formula should not be the problem. So... it's a mystery. Between this issue and the inability to tolerate normal volume via her feeding pump, we are struggling to keep her weight on.
As an infant and toddler, she dealt with cyclical abdominal migraines - - these transitioned to actual migraines as she got older. However, anytime Gracie isn't feeling well it manifests in her stomach. It's difficult to explain what happens and it's really torturous to watch how uncomfortable she is and how helpless we are, unable to give her real relief. There are times when her stomach is so sensitive that we can turn on her feeding pump at a rate of 15ml/hr (that's half an ounce over an hour) and she will react by retching. When this happens, we can sometimes give her ibuprofen and it will do the trick. Most of the time, however, we have to stop feeding her for a few hours and then start back up with just Pedialyte and move to a mix of half formula, half pedialyte and then work our way back to full formula. This usually takes 24 hours. If we go too fast, she gets worse and we have to start all over. She has lost more than 3 pounds and is now below 30 pounds. The weight loss coupled with the inability to get all her calories all the time has led to a set-back in her gross motor development. She is just now getting back to the level she was at in her gait-trainer (walker) in the Spring of '06.
Last month she had a Gastric Emptying Study that was less than impressive, according to her doctor. We fed her just one ounce of formula mixed with small amount of radioactive dye and for an hour, a machine took pictures of her gut to watch the digestion progress. (Needless to say, this was not a pleasant experience for her. Because sedation slows down motility, it is not used in this type of study. So, Gracie was wide awake and strapped to a table for an hour with a machine just inches from her face and body. She was terrified. John sat at her feet, giving her joint compressions & massage and I sat where she could see me, signing to her, suctioning her every couple of minutes and trying to help her understand that we couldn't go home yet.) This is not the first time she's had this type of study - - but the last one was before she had her trach, so she was only about 15 months old... all of them showed similar results.
Also in the last year or so, her GI doctor has taken three "peeks" at her stomach and bowels and has also biopsied the inflamed tissues all through her digestive tract. She keeps telling us that it doesn't look good in there... that we have work to do to get her better, but there is no real "plan of action" and we are feeling a little lost. We feed her the most elemental formula that is made - - it is broken down so that the gut has to do the least amount of work to digest it. This has not helped. We have tried numerous medications... to no avail. So, now her doctor wants to take another look and do a full colonoscopy. We told her "no, not yet." We want to give some other, more natural options a try. We wonder if her digestive tract actually needs to do more work. We might be wrong... but it can't be any worse than the multitude of medications and procedures that have done nothing to rectify the situation. So I am researching blended diets ("real" ingredients blended down to pass through her feeding tube) and hope to give this method a shot by the first of March.
Please keep your fingers crossed.