It' good to hear that they got to the bottom of the problem anyway.  It will probably take a while for something like that to come right.  Especially if things have been stressed in that area.  With Kyle it was a case of immature development of that muscle and it started to come right after the sixth months of age.  However, I am not really clued up on knowledge where stress is concerned in the muscles of the osophagas.  That's probably what the diet is about---keeping her comfortable why the muscle's repair themselves which probably take time.  I know what you mean about the coughing though.  Also any sever vomiting illness can put quite a strain on the tummy muscles or the stomach itself.   This can be fatal if one has a ulcer as our family found out when my brother was 14 yo.  One always thinks of the stomach as a resilient organ as we know it has strong acids to help with digestion.  However, when there are weaknesses in that area such as in your daughter's case, it can be very troublesome. 

My partner has problems with acid all the time and we cannot figure it out at all.  Sometimes I think there is a tendency to go out and pop to the chemist instead of to your doctor with things like tummy upsets or indigestion and not go to get the problem sorted.  My Mother suffered for years and when she went to the doctors he prescribed her a course of anti-biotics and she never had a problem again.  it was a bug in her gut!   I once read that you have to be careful buying and taking ant-acids all the time as they cut the natural stomach acids back and therefore it leaves one less able to deal with some of the really nasty tummy bugs that crop up occasionally.  The acids usually knock most of those on the head and usually half the things that we eat that have any bacteria, the stomach acids kill this and saves us from the tummy upset's that would occur.  However, taking an ant-acid prevents the stomach acids from doing this to a certain degree which leaves us a little more vulnerable.  So what I would say is make sure that she does not share drinks with other's or that everything you eat is well cooked for a little while until she is having the ant-acids reduced back a little.    It will save any vomiting illness and putting any more strain on the muscles that have been stressed. 

Regards