I am confused about allergy vs. intolerance. I understand that our children may be sensitive to corn, soy and other foods as well as gluten and casein. Does this mean that they will eventually start turning these foods into the morphine-like compounds too? If this were the case, would they show up as an allergy on a RAST test? Or were our children were always allergic to these foods (a regular allergy that may cause behavioral changes in our children), and we just didn't know because the gluten and casein were hiding the allergy.

To a traditional physician or allergist, "allergy" is used to describe a reaction of the IgE part of the immune system, resulting in hives, swelling, or breathing problems. However, the words "allergy" and "intolerance" are often used to describe any inappropriate reaction to foods or substances that should normally be harmless to the body.
There are at least three different ways that a child with autism may have a problem with a food like gluten or milk, and it's important to understand the distinction:
1. An IgE ALLERGY that results in skin problems, hives, swelling, breathing problems, etc. This can be tested using a skin test or blood test.
2. An INTOLERANCE (usually mediated by the IgG or IgA part of the immune system, or by an enzyme insufficiency such as lactose intolerance) that can result in more varied or vague symptoms like discomfort, stomach problems, sleep problems, joint pain, ear infections, or hyperactivity and behavior problems. Sensitivity to these substances can be tested with an ELISA blood test.
3. PEPTIDUREA (peptides in the urine) that is caused by the inability of the body to properly break down certain proteins. It is hypothesized that certain peptides, notably from milk and wheat proteins, are plugging into the opiate receptor sites of the brain and disrupting brain and nervous system function. Urine testing for this is still experimental, and many parents believe that the best way to find out if this is what is causing a child's autism is a strict trial period on the GF/CF diet.
In the GF/CF diet, gluten and milk are avoided because they are strongly suspected of having such a direct pharmacological effect. When these proteins are only partly broken down, some of the resulting fragments can be strikingly similar to morphine, and act in more or less the same manner. (This type of reaction can co-exist along with a classic type of allergy towards the same foods).
Recent research indicates that protein from both corn and soy (as well as protein from blood and spinach) could also contain some molecule sequences that could - if the patient had an enzyme deficiency - be broken down into something closely resembling opoid peptides.
Products made from soy or corn will also often contain metabolic end products made by microscopic organisms like bacteria, molds or fungus. Some of these are suspected of being harmful to a small number of people who are genetically disposed to autism. The amount of danger will depend on individual conditions AND on the quality of the corn or soybeans used in the production process. Soy OIL (lecithin) may be worse than most other soy products, since this product will look and taste okay, even when made from moldy raw material, and since the "bottom grade" of the harvest tends to be used for it.
Some people also think that one of the natural pigments in corn (lutein) might cause problems for reasons that are not properly understood (see: "Sara's Diet"). This must be regarded as highly specualtive.