I wanted to chime in on a few things about her health, maybe offer some help or suggestions.
You mention checking her IGA levels. IGA levels have to do with your immune system. If you are IGA deficient, you don't produce immonuglobulin A which weakens your immune system. So you are more prone to ilnesses, it takes your body longer to heal, to respond to antibiotics for infections, etc. You said they thought you should see an Immunologist...what is that? I've never heard of one, and i'm wondering if this is something we should be enquiring about since our daughter has an IGA deficiency.
An Immunologist is a doctor that Specializes in the immune system. Korissa is always sick. She has been since a baby. Started when she was 6 months old. She has been in the hospital many times due to infection and high fevers. When she was 3 she saw a GI and they ran some blood test and her IGA was low and it stated in report that she should see an Immunologist. This message never got to me. To this day..she is sick at least every month with sinus stuff. Some with high fevers other without. The Ped is now ordering these test again to see if her IGA is low or not.
My daughter has GERD as well, and is currently being treated with Zantax, (and has been on Prevacid at the same time, but they managed to wean her off that in the summer as they were trying to decrease the amount of meds she was on) and Domperidone. She was also on Metaclopramide, but the dose wasn't enough for her, but she was too small for the dose to be increased, so back to the Domperidone. That has worked great for her. She has been on Domperidone since she was a baby, but was taken off for about 6 months to try the Metaclopramide since it seemed to stop working. So they wanted to introduce something new. Has she ever been on either of those?
We have tried Zantac, but that didn't work. Hopefully the Nexium will. Kylee has DGE and has been on Domeridone(this is a DGE med..right?) but did nothing for her. She was on Metaclopramide(Reglan) but that had horrible side effects on her. They also didn't want her on it because of her past seizures history.
What is taking for her bowel issues? Is she on any sort of regular meds? My daughter was on Lactulose, and while that worked well she was having a very tough time tolerating it because she needed such a high dose. Shes back on Peg 3350 (was on it for 3.5 years but came off of it because they wanted to try the Lactulose), and it works great. She also takes Senokot and the combination of both of those work great. Her Paed doesn't like her on Senokot, especially long term, but her bowels freeze up without it, so for now the negatives of it are somewhat ignored for the fact that she needs it. We can't miss a dose of either of those meds (she gets them each twice a day, sometimes the Peg she'll get 3-4 times a day), because you can tell a difference pretty quickly.
What med has she not been on...Lactolose causes horrible cramps so does all Senna products. When she is on them she goes lethargic and her ketones goes sky high. Enemas only get whats at the bottom and not on top, so it relieves for a day than we are back to square one. I don't even do them anymore. It's just more trama on her. It takes 4 of us just to hold her down. What she is on right now is 25g of Miralax 2x a day. and we do Golytely 2-3 times a week as a maintenance.
As for the bacteria you are talking about, is it bacteria overgrowth in her small bowel the are thinking? My daughter has this, its called Blind Loop Syndrome. My daughter goes on antibiotics for the first 7 days of every month, and it makes a huge difference in her stomach distention. Her stomach bloats so much (whether her bowels are cleaned out or not), and once she starts her week of meds, you can tell that something is being cleaned up inside because she looks much more comfortable. Her Paed has even talked of her being on them longer then 1 week (or alternating weeks), but for now they want to see how she does. She goes back on her antibiotics next week.
I believe thats where they are thinking or Korissas stomach. The GI just said Breath Test to see if she has Bacteria overgrowth. Is their another way to see at home if she has this? I know Kylee can get it since she had a Roux En Y done.
Not sure if any of that helps. I'm sorry things are so frustrating lately, you have every right to have down days. Try not to beat yourself up about it.
Dust and try to get some much deserved rest (Okay, I know, I KNOW!!!!)
We have been praying for you guys. I hope you get some concrete answers soon. 
The gj-tube goes in to the small bowel where the g-tube goes in the stomach. She couldn't handle anything in her stomach when she had an ng-tube so they advanced her to an nj-tube with much better results. So when it came time for the more permanent tube, it was decided she would have a gj-tube rather then a g-tube. She was refluxing way too much with anything in her stomach and she was throwing up all the time. We know part of it was the GERD and a big part of it was her delayed gastric emptying.
