For a standard NOBO, I think your UL inner down jacket is fine, no need for the beefier down jacket; if you're cold in camp, crawl into the sleeping bag.
Shirt: I liked having a light, loose, button up shirt with good SPF that I wore just over my skin all the time; backup and "town" shirt was a short-sleeved smartwool shirt (doesn't smell). Maybe for the Sierras add a capilene 1 long sleeved shirt (?). Or maybe not --- a windshirt can do a lot when you just keep moving.
Shorts: it's a "style" thing; I personally always wear long sleeves and long pants (keeps off sun, brush, bugs), and use shorts as backup underwear and to wear in town when washing clothes.
Rain pants, wind pants: I suggest that you carry neither. Maybe a rain skirt, if you can get or make something quite light.
Insulated pants: I suggest that you carry neither. Maybe consider a pair of very light silk or capilene 1 longjohns if you're concerned, then mail them home when you're not using them ...
Hat: personal preference, but do provide some way for the straw hat to not go sailing off in the wind.
I would bring a balaclava and carry it until done with the Sierras, to sleep in.
Glove liners, and I suggest some sort of fairly light mitten --- the OR PL 400 is a good choice. Then maybe a shell, but perhaps only for WA state. For that amount of distance, you could just get a couple of bread bags and wear those over your mittens.
Real, 100% wool (or close to it) decently thick socks for the Sierras, two pairs --- one to hike in, one to sleep in. One pair before and after the Sierras. Apart from that, whatever you're inclined to.
Shoes: no one can help you find the right trail shoe, but you. Lots of threads on this topic, search this (and perhaps other) forum(s) to find many and often conflicting comments about what's "best".
One thing that I like to bring is earbags (google it). Little units that snap on to cover your ears. They make the cold windy times a lot more pleasant.
If going with trail runners (which is all you need, including in snow), you might consider goretex socks for the Sierras, and maybe WA state. Size them up to fit wool socks inside them.
Consider some sort of sun gloves; there are some that are explicitly for this (such as those made by Coolibar), or perhaps you can find something light that breathes well elsewhere. Especially if you use trekking poles, the backs of your hands can get quite burned. I personally like covering up and hence not using a lot of sunscreen in the south (and elsewhere). Lightweight, quick-drying loose clothing.
Consider a pair of bread bags as emergency VB socks, and for use in camp to keep your dry socks dry when you put them in your wet trail shoes.
Best of luck!