My “baby” is now nearly 5 but I remember those months well. The toughest of all. Here are just a few thoughts – but just to know that I don’t know about feeding tubes so some thoughts might not be appropriate…
GI health is so critically important – gut issues can appear to be lung issues, coughing, etc, so you really want to keep checking the GI. “Coughing and congestion” could easily result from a GI imbalance.

I did stool tests over and over. It is so easy and you can keep an eye on the GI bacteria. The analysis I use from Doctors Data give you “susceptibility” of the bugs to natural remedies as well.

I added a hefty dose of probiotics (I think this could really be helpful to you especially as abx totally screw up the bowel flora and additionally yeast loves GSH as much as the rest of the body) , and GSH. Both sooth the gut inflammation. The GSh will protect the liver too. Reduce inflammation and the weight gain will come…I used lipo GSH with my baby because it was once per day and a liquid I could squirt in the cheek.

Mucolyxir is for use with babies. It is a “natural “ pulmozyme and well as an immune boost. Again is 2 drops on the tongue, so baby friendly.

CPT is great – but the position of tilting the head downward has shown in research to cause problems in some cases with stomach acid – a level position has proven to be as effective. This was our case too. Just FYI.

I didn’t address the staph specifically at first. It is gone now.

I think you are being really smart in looking for alternatives and in thinking that healing the immune system would get at the core of the issue.

If I were you I would get a naturopathic doctor to guide you in healing the GI. There are baby friendly homeopathic remedies to balance gut Ph (enzymes won’t work well in the wrong Ph), natural bronchodilators, and immune boosters. ND would also be the one to order the stool test kits for you and could help you pick an appropriate probiotic. A regular MD will probably not be helpful in boosting the immune system, which is so vitally important with CF.

You can totally do this and get on track!

http://www.naturopathic.org/
http://doctorsdata.com/test_info.asp?id=16
http://www.springboard4health.com/store/more_arg_mucolyxir.html
http://gshnow.com/
http://readisorb.com/