Wow, those are some good questions. I too am hoping that others will be able to help out on these. What I do know for sure is that the liver is always responsible for the assimilation of food in the body, for detoxifying the body in general, and food allergies of any kind are always the result of an overtaxed liver. So that is the organ that is always affected, in every case. A stressed Jupiter or a Jupiter in hard aspect to other planets can reflect what you are describing.
Once the liver becomes overtaxed via toxic or synthetic foods, any other body systems can be affected, depending on the lifestyle, karmic background, and congenital weakness(es) of the person in question. But those with wheat or gluten allergies usually also have a negatively impacted mind/brain: chronic depression, negative thoughts of futility, angst, malaise, etc. This is especially true when Jupiter is in hard aspect to Saturn, or even Mercury.
Of course, there are karmic reasons for being born into a body that does not assimilate food properly. I believe I remember Wolf saying once that all allergies are the result of undigested or unresolved emotion; with the liver, the corresponding emotion is usually internalized anger or rage. This would point to Mars and its house, sign, and aspects.
In terms of remedies for such a thing, as I posted before, the liver is clogged in every case, and so should be flushed. The liver (and thus the body) can be cured of food allergies, but care must be taken not to revert back to the consumption of processed food once this is done.
I did not learn the liver-flush information or the liver-anger correlation from EA, so if anyone knows of EA correlations to this phenomena I too would be so interested to know. And, Bradley, I hope it's okay for me to have added two more cents to your questions, for whatever it's worth.
Love and blessings (and happy new year!),