Shelter:
I would hate to spend a rainy night in a waterproof bivy, so I would take something else. You can get quite a few waterproof and bug free shelters for about that weight. I would look into one of the Tarptent Models, maybe the Protrail. You might not need it in the desert but you will likely need it in the PNW. I know an AT hiker that thru hiked the AT with an MLD event bivy so it can be done, but when he hiked the PCT he changed to the SMD Gatewood Cape (which would be good option except it doesn’t work well for users over 6’)
Sleeping:
I would want more than a 35* bag but that is just me, and a bag is a big investment. If you have the cash you might look used for a nice 20* down bag like a WM Ultralight or Marmot Helium, or even join the ranks of quilters with an Enlightened Equipment quilt. If you chose to get a new bag or quilt, I would scour Gear Swap here as there are good deals to be had.
I would not take the Silk Liner. They add negligible warmth, get tangled up and light baselayers do as good of job at keeping your bag clean and are more versatile.
21oz for sleeping base layers is a LOT. There aren’t any baselayers that add a whole lot of warmth, and that is the weight of a whole other sleeping bag. I am in the camp where I like dry and clean baselayers in camp and to sleep in but you can get them pretty light. Another OR Echo shirt would be a good option, or a 5oz Patagonia Cap 4 shirt will actually give you some warmth. There are generic versions out there that are cheaper than the Cap stuff. I think you can do top and bottom for 10oz or less and be able to use it as hiking base layers if you really needed it.
For sleeping socks, I usually alternate socks with my hiking socks in more arid places. If I am in a really rainy environment I keep one dry pair for sleeping and put on the wet pair every morning. Usually if I can’t get a pair of socks to dry out, a dry pair would be soaked in just a few minutes anyways. You could take a three or four pairs of no cushion wool socks for the weight of your sleeping socks alone.
Are you sure about the weight on that Ridgerest? My 72×20 RR is 12.75oz
Water:
I would ditch the Nalgene bottle. Just use Gatoraide bottles you can get from a gas station. They last for hundreds of miles (maybe more, I never tested to see just how far one would go) and are around 1.7oz each for the 32oz size, but they also make 20oz and 64oz versions.
The first need is a world class filter that I would not have hesitated to take to a 3rd world country ten years ago. The PCT is not a third world country, and its 2015. If you are worried about viruses, try a steripen, if you like a filter try a sawyer, if I were you, I would use Aquamira. If you ever decide to hike the CDT I would use something more than just aquamira, but for the PCT (or the AT) that is it.
For hydration bags, I would go with multiple 3 liter platypus bags.
Vargo Bot: Interesting product. I never knew that existed. It’s really pricy though at $100, so if you haven’t already bought it that money would be better spent on a shelter or sleeping bag/quilt and just get an Kmart Grease Pot or Anti-Gravity Gear (Open Country) Anodized Aluminum pot and carry an extra Platypus or Gatorade Bottle.
Other Clothing:
8.6oz for 1 pair of boxers? I would verify that weight, but you can get boxers a lot lighter than that (My ex officieo ones are 3oz/pr). You might be able to without a spare pair if you stop in towns for laundry often enough. That is a personal call.
For your rain jacket, I think you would feel stupid carrying a 17oz rain shell through the desert and in the Sierras (I think we all have felt stupid for carrying something before). I would suggest changing it out for something lighter like an Luke’s Ultralight eVent Rain Shell at 7.5oz, or if you are on the cheap, a dri-ducks jacket for the desert and sierras and have someone mail you your heavy jackets for the PNW. I think I would use the weight saved here to add rain pants (something light ~6oz or less – personally I would think the Lukes UL Gore Tex Rainpants)
I would take a puffy instead of the wool sweater, but that is just me.
Nutrients:
I am pretty much going to leave this one alone, but if you are going to take all of that, I would try and set that up in smaller maildrop quantities. I mean two pounds is a whole days worth of food!
Misc:
The headlamp is a little heavy in less you plan on night hiking, but thats a personal thing
I would change out the heavy pack towel to a bandana.
Things I would add:
Sunglasses – The sun in the desert and the sierra is brutal. A cheap pair will do
Hat (for sun) – see above. My favorite is the OR Sun Runner, but you can even make your own version with any running hat and a bandana. You want to protect your neck and face from the sun.
Rain Pants (or wind pants) – You may want them in the Sierra or PNW
Windshirt (some people like them others don’t)
Camera – Do not take this trip without a camera.
First Aid Kit – nothing big – Advil, Imodium, Benadryl, and some Likotape P (sp) for blisters are probably enough. Under 3oz.
Stove – I would take something here. I would do an alcohol stove or esbit if you don’t plan to use it daily.
Fire Starter – (I am not a survivalist, I am just thinking Mini- Bic @ 0.4oz)
Cutting Tool – (again not a survivalist – I am thinking something to cut tape and cut your toenails as much as anything.) I would think a small pair of nail clippers or a small 0.6oz swiss army knife with the scissors. I often take short trips with no cutting tool, but I am not sure if I would want to hike the entire PCT without one.
Cordage to hang food? (bear can will be needed in the sierras)
Head Insulation – I like a 100wt fleece beanie for sleeping, camp, and cool mornings/says.
Map/Compass – I am not sure if you would need a compass on the PCT, but a small one wouldn’t hurt, but I would take some sort of map.
Smartphone??? – I hesitate even putting this, as I would never take one on a shorter trip, but on a multi- month trek it might be useful to have. You could use it as a camera and keep connected with home (in towns, etc.) I don’t think it would work much from the trail itself.