Nice list. It's clear you've been doing some thinking. I too would cut down on the number of stuff sacks. I’d lose the Chamois for a large bandana, larger than those in camping stores which you can find elsewhere online. I’ve found a bigger bandana is more useful in a lot of areas and it is a more releastic size for an arm sling or something similar if you had to make one. I’d lose the Patagonia stuff not because it isn’t good but because I’d worry about smell and cleanliness issues. I’d go with something in the Merino Wool line. I’d lose the Tikka and replace it with something like the eLITE if you want a headlamp or just a clip-on like the Photon Micro-Light II. I’d make sure you’ve got a good plastic bag for your bear sack since it is otherwise just mesh. I’d consider switching to something like the Western Mountaineering Caribou MF for the bag which you could also use as a quilt (if you can get your hands on a quilt instead…use it). Personally, because I think it is warmer (although I’m not sure it would be absolutely necessary), I’d switch to something in the BPL Cocoon line instead of the Montbell U.S. Down jacket even though the Montbell is a good jacket (hard fit with some people though). Even though it won't rain much (not to mention you'll be covered by "the green tunnel", I didn’t see any rain pants (unless I missed it). I’d consider the ULA rain wrap and maybe a top from DriDucks or similar to lighten more. The wrap is great for modesty and “airing out” when showering or cleaning up, and in a pinch it could be used as an impromptu ground cloth. Many people on this site also use SmartWool Adrenaline socks. In most cases, I love SmartWool stuff…but not with these socks. They pill and wear very easily. Consider one from the Darn Tough line. Although I think your packs are a bit big, I wouldn't go with a frameless option. I doubt the folks suggesting a frameless pack have ever done a thru-hike, or if they have, they didn't carry the weight required for multiple days without resupply. Flatly put, food is heavy. The 100 mile wilderness in Maine is a good example of where I'd like to have a frame, even if minimal. In these situations, you'll want something to bring the load to your hips. I use a ULA-Circuit, but for the AT I would either use the ULA-Circuit or ULA-Conduit as others have said. You won't need sunglasses as you'll always be under a green canopy and a hat is always great to cut down on whatever gets through, wick sweat, and be a good first line of defense against spider webs. I also wouldn't put much faith in the comment by someone who said not to carry more than 2 litres. In summer especially, water isn't necessarily that available as many of the smaller sources do dry up...although you are never more than a few miles away from it..but a few miles may be too much. Either way, personally, I'm a big fan of water and I'd consider 2-4 litres. One great resource I never hear people talk about it a simple nylon mesh to serve as a prefilter for the bigger water stuff so you could easily get by with just AquaMira. I've found great luck in the tiny and inexpensive nylon bags found at Walmart in the wedding section (like the kind you put chocolates in and place at each table setting). They work amazingly. Consider gaiters too. There is little more annoying than having something in your shoe.
By the way, nice website. Keep thinking big and clearly.