I believe first and foremost you need to heal the gut wall - a leaky gut is primarly responsible for most allergies, because it allows food particles to enter the blood stream and cause symptoms typical of allergy sufferers (hives, rashes headaches, itchy skin). A healthy gut will not allow this to happen. Dairy and meat can create a lot of the allergies because a lot of animal derived products may contain specific proteins that immediately trigger a reaction. Again a healthy gut with strong digestion will not allow this to happen as protein is broken down into aminoacids to be absorbed by the gut wall.
Leaky gut syndrome can be caused by a lot of factors but one thing is for sure - nutritional deficiencies. The gut wall is made up of mostly protein (formed by aminoacids) and with the wrong diet comes weakening of the digestion, and this can create nutritional deficiencies that may not allow your body to properly detoxify, inviting pathogens to make of feast out of the toxins. A lot of people can eat crap if they have good digestion and good nutrition absorption because it allows them to properly detoxify the junk (however with time it will eventually wear you down to chronic diseases).
So leaky gut is hinting towards weak digestion and nutritional deficiencies because your body is lacking the nutrients to heal the gut wall. The problem with this is that even if you eat right, you may not be able to absorb things properly and further create allergy symptoms - although you may need a lot of the protein, if you cannot break it down into aminoacids, it may give you more allergies (the majority of food allergens are high protein sources).
So by providing nutrients in its most basic and absorbable form (requiring no digestion) can do wonders at this stage, while stregthning the digestion with digestive enzymes, betaine HCl, etc if necessary (these may not be tolerated in high amounts if your inner digestive tissues are so weak that may be too sensitive to this).
Free form aminoacids can be absorbed quickly and immediately put to use and start healing the gut wall. Bear in mind that if your digestive system is fragile it may mean that other parts of the body may be starving for the right nutrition as well so your body will use the nutrition, like AAs, based on priorities.
It also sounds like you may have no good flora left in the colon as the increased transit time suggests. This allows pathogens to crowd the digestive track all the way down to the colon - probiotics may help colonize the colon and displace pathogenic species - they are also involved in specific nutrition production like certain B vitamins, so you may be lacking this as well. Bear in mind that until your gut is healed and allergies subside, anything that you may take may enter the blood stream and cause more allergies. Plenty of free form amino acids, efas, ionic minerals and other easily absorbed nutrition can work great. Glutamine is traditionally used to heal gut wall (non essential amino acid), but primarily supplying the essential aminoacids may allow the body to convert to whatever other AAs it needs.