Some random thoughts on this.
Have you put 'Bears' into you decision making process? lol.
Options are, don't hang food (popular with thru hikers staying in the shelters), hang food, use an ursack.
I used to hang, now I have my trusty ursack (from REI no less).
If you hang, I recommend some sort of dyneema wire (rope) from lawsonequipment. I use something 'slick' so it doesn't drag so much on the tree limbs and brush, and, after a very tough lesson learned (I'm might have posted a story about this somewhere here, involving night time and adult beverages, and general forgetfulness), a cord that is reflective to the beam of your headlamp. pro tip: carry a very teeny stuff sack, maybe 3-4", put a rock in that, then clip with small 'biner' to your cord, then toss over limb.
All that said, I now use an ursack exclusively, no odor liner, except in the Sierra Nevada where a canister is required.
On the clothes bag situation: I bought this great stuff sack from REI that is lined on the inside with a cloth material, so at night, you turn it inside out, re stuff the clothes, et voila' ! a fantastic pillow!
I always recommend lining your pack with something like a trash can liner so EVERYTHING is water proofed, so I haven't been worrying too much about waterproof stuff sacks.
Although backpacking in Iceland last summer I was pretty paranoid, so I carried some 1 or 2 gallon size zip locks (from the Dollar Store).
I also use very large zip locks in my top pack compartment (those never stay dry in a rain) and for my camera.
Lastly, I also recommend only 1 set of spare clothes. That 'dry set' is for camp, after you arrive soaking wet from an all day rain. Then change back into your wet clothes the next day and walk them dry. Unless it's freezing - and - raining, then you're screwed. Only choice is to put on your dry clothes with enough rain gear to keep them dry, and hopefully because it's cold, you won't get your clothes wet from sweat. Your dry clothes and sleeping bag are your last line of defense from hypothermia.
And lastly, lastly, unless you are just in love with walking in tree tunnels all day, everyday, I recommend "go west young man!", get out of the tree tunnels and walk all day with mountain views and the horizon all around you, on the PCT, the JMT, the CDT or where I go, Bridger Wilderness in Wyoming.
Oh yes, sorry, one more thing, If you haven't already, check out whiteblaze.net, all things AT. (and tree tunnels) 😉