I haven't had to figure logistics for a thru-hike, but I've been working with gluten-free dairy-free backpacking meals for the last 9 months. Yes, you will have to make a lot of your own food. Pack-It Gourmet does have gluten-free meals available, but that's the only company I know of off the top of my head. I was already making all our backpacking meals before that anyway, so it wasn't too much of a stretch to figure out what to do.
Get a dehydrator. That will pay off in making dehydrated meals that can be packed ahead of time. That and a Food-Saver, and you can make meals, rather than having to rely on commercially prepped meals. Pack-It Gourmet will mail mail drops ahead, and you can order from their meals, or from their grocery store and get basic materials to mix-and-match meals. Lipsmackin' Backpackin'was written by folks who section or through hike the Pacific Crest trail, and lots of their recipes can be adapted with only a little tweaking. Their are two approaches: Make actual meals ahead of time, or have recipes that can be variations, like having noodles and figuring out a Spaghetti variation, a Chinese variation, a Curry alternative, etc. and just having easy alternatives to switch out.
Breakfast is the hardest. Gluten-free rolled oats are available, and at least you can eat eggs, which isn't on my list. I've been experimenting with pumpkin, sweet potatoe or butternut squash "bark", using backpackingchef.com's techniques for dehydrating.
Quinoa will probably be a big source of food for you, to help with protein as well as being gluten-free. There have been a few discussions on the Food and Hydration section on how to cook it on the trail. A Taste of Thai has rice-based "ramen" packs that can be used as a base for noodle dishes; not all the flavors are dairy-free, but most of them, just don't use the curry flavors. They are also MSG free, and their flavor packets are free of anything except soy, which you didn't mention as an allergen, so I assume you can eat it. Tofu can be dehydrated.
Dairy can be a little harder. Obviously, cheese is right out, and cheese sauces as well. I just found recipes for making cream soup bases using dairy-free milks, and plan to use that to substitute in recipes from Sarah's trailcooking.com web-site and book. She eats vegetarian and vegan, so her website is a good resource, as is Laurie Ann March's books A Fork in the Trail. Her second book, Another Fork in the Trail, is specifically written for vegans and has some gluten-free recipes, and others that can be adapted.
The biggest problem that I haven't found an answer to is tortillas for backpacking. The gluten-free alternatives don't wrap well when cold or when stored; if you spread peanut butter on them, then try roll them around the contents, they shred and fall apart. En-r-G gluten-free crackers aren't bad, just plain, but they need careful packing to not crumble in the pack. Gluten-free breads are frankly nasty, dry and crumbly. Every single one I've tried, store-bought or homemade, is just "almost good". The home-made ones are good fresh from the oven, but once stored they crumble and dry up.
Google Paleo backpacking--by its very nature Paleo is gluten-free, and there are some options out there. Restricting meat might make it hard over the long stretch for protein, but variation will be your friend there. Is fish an alternative? Tuna and smoked salmon might be big protein sources.
I've considered how to do this, as a thru-hike is a dream of mine. I'd break the trail up into sections between mail-drops, counting how many days I think I need to get between them. It will look a lot more do-able. Figure out somewhere between 4-5 meal alternatives-4-5 dinners, breakfasts, lunches. Repeat them in rotation between sections, so that you have variety in each section, but have a manageable number of alternatives to prepare at home. Research possible health-food stores ahead of time along the trail, as they are more likely to have gluten-free options that can be purchased fresh. Fred Meyer and Safeway are usually pretty good for finding options, and surprisingly Wal-Mart isn't bad either. Relying on convenience stores will be a bad idea. Coordinate with Pack-It Gourmet for drop-shipments of dehydrated veggies. Carry ghee for butter flavor, and/or Earth Balance or learn to like olive oil or other oils as alternatives. minimus.biz is good for small packets of stuff for flavors as well.
Just off the top of my head that's the best advice I've got. Think of it as an opportunity for creativity. There have been several posts on the Food and Hydration section, including my panic freak-out on how to prepare for a week-end backpack right after being diagnosed. Just try to test out recipes before you go--there's nothing worse than hiking a long distance only to face a dinner you don't like!