I'd like to flag up two issues in the article you posted dolfrog:
First is the part about treatment for GERDS where Surgical therapy or prolonged acid suppression are the suggested threatments.
Below is a bit taken from the GAPS book where she describes that low stomach acid production is common and can give GERDS like symptoms. In these cases the treatment described in the paper either wont fix the root cause of inflammation (in the case of surgery) or just exacerbate the issue as in the case of acid suppression.
NCM says in her book
"1.Hypochlorhydria
People with abnormal gut flora, almost without exception, have low stomach acid production. Toxins produced by overgrowth of Candida species, Clostridia and other pathogens have a strong ability to reduce secretion of stomach acid.
?........
Of course, most of these microbes love to eat carbohydrates, particularly the processed kind. The digestion of carbohydrates starts in the mouth with the action of saliva. When the food reaches the stomach normally stomach acid stops this digestion. So, carbohydrates have to wait until they arrive at the duodenum to be digested. But in the stomach with low acidity, overgrowing microbes start fermenting dietary carbohydrates, often with the production of various toxins and gas, which can make it very uncomfortable for the GAPS child or adult and make them refuse food. Accumulating gases cause excessive belching and burping. Apart from that some pathogens grow around the sphincter muscle at the top of the stomach. This round muscle normally separates the stomach from oesophagus and does not allow food to go back up. Pathogens, growing in that area, and the toxins they produce, partially paralyse the sphincter muscle which causes reflux: regurgitation of food back up into the oesophagus. Even with low stomach acid production there is some acid in the regurgitated food, which burns the walls of the oesophagus, giving the person typical symptoms of ?acid indigestion?. Antacids are usually prescribed for acid indigestion and reflux, which may alleviate the immediate symptoms, but in the long run make the whole situation worse as they reduce stomach acid production even further.
So, what do we do?
I believe that GAPS patients need supplementation with stomach acid. The most physiological preparation available on the market is Betaine HCL with added Pepsin?......
Apart from supplementing stomach acid there are natural things we can do to stimulate the body to produce its own stomach acid. Cabbage juice is one of the strongest stimulants. Having a few spoonfuls of cabbage juice or a small cabbage salad before the meal will help to digest the meal. Sauerkraut and its juice are even stronger. A small helping of sauerkraut or a few tablespoons of its juice will prepare the stomach for the arriving food. Having a cup of homemade meat stock with your meal will also help increase stomach acidity.???."
Here is a link to radio interview with a woman who had GERDS. She was treated for silent reflux with PPI to the detriment of her health. www.blogtalkradio.com/gapsjourney (It?s the one titled Maureen & Simon)
The other issue I have is where it talks about the treatment for Chronic Diarrhea and it?s possible different causes; lactose intolerant, food intolerences, gluten intolerance, bacterial or yeast overgrowth.
If the gut lining is damaged as it is believed to be with those suffering from GAPS then all of these causes will more than likely be an issue. If they are not viewed as a whole but treated individually i.e. try removing diary for a bit, try removing gluten for a bit then the result will be the condition is still there and only one of the numerious irritants has been removed so at best the symptoms might ease but not disappear.
This is a good piece that explains the fundamentals of the GAPS dietary approach. Taken from here www.thehealthyhomeeconomist.com/2010/07/heal-your-autoimmune-disease-now/
"What Foods Do People Healing Their Guts Need to Avoid


At first read, the GAPS diet can seem quite complicated. In actuality, it is really very simple.
There are primarily two types of food molecules that folks in the process of healing their guts need to avoid:
Disaccharides
Starches
Disaccharides, or double sugars, are present in many carbohydrates including ALL grains. The compromised gut is unable to digest double sugar molecules because the lack of beneficial gut flora compromises the function of the enterocytes.
The enterocytes are the cells that reside on the villi of the gut wall and produce the enzyme disaccharidase which breaks down the disaccharide molecule into easily absorbed monosaccharide molecules. When the enterocytes are not nourished and strengthened properly by adequate beneficial flora, they become weak and diseased and may even turn cancerous. They do not perform their duties of digesting and absorbing food properly.
The critical importance of the enterocytes to health cannot be overstated!



Weak and diseased enterocytes also have trouble digesting starch molecules which are very large with hundreds of monosugars connected in long branchlike strands. People with weak digestion due to an imbalance of gut flora and messed up enterocytes have a terrible time digesting these complex molecules leaving large amounts of it undigested- the perfect food for pathogenic yeasts, bacteria, fungi and other pathogens to thrive upon.
Even the starch that manages to get digested results in molecules of maltose, which is ? you guessed it ? a disaccharide! This maltose also goes undigested due to a lack of the enzyme disaccharidase and becomes additional food for gut pathogens.
The Bottom Line
Therefore, all foods containing disaccharide and starch molecules must be removed from the diet of a GAPS child or adult in order to allow the enterocytes to strengthen and heal the gut wall.
Dr. Campbell-McBride MD writes that clinical practice has shown that given enough time, the gut usually will again be able to digest these foods without any ill effects (aka, autoimmune disease) to the person consuming them.



The GAPS Diet is not a forever thing. It is a temporary measure to heal the gut wall and restrengthen the enterocytes so normal life can be regained without the burden of autoimmune disease."