Nice list. I agree that the bivy/tarp combo might be a bit of overkill, unless you just want to set up the bivy only, which you would be able to do a lot of the time along the trail (or even Cowboy camp), particualrly in So Cal.
As for the NeoAir, I am completely biased, but this is the one great piece of gear that I would absolutely carry with me on any thru-hike. It allowed me to have a great night's sleep. Otherwise, as a side sleeper, I'd awaken several times a night from the pain in my hips. YMMV.
Bear canister is required in the Sierra - just something to think about. I hung my food bag maybe twice on the whole trip. I just slept with it and used OP Sacks.
Water capacity - without quesiton, be prepared to carry at least five liters of water with you in Southern California. It's shaping up to be a low snow year and as I recall from a normalish year, there were some very long stretches where there was no great water supply. Combine that with high temps, and you get the picture.
Insulation - I would absolutely carry an insulating layer. Yes, much of the time it's not necessary but when you need it, there is reallly little substitute. The Sierra can get snow in late spring - and it can get quite cold. In the northern section of the trail you can run into a lot of moist, cold weather, even in summer. It's very easy to underestimate the difference between cold Sierra and cold Washington. I guarantee the later will feel colder because the relative humidity on the west side of the Cascades is so much higher than the drier climes of the Sierra. Also, weather tends to stick a round longer.
Of course, should you blaze the trail quickly, and hike through Washington in August/early September, you may find it pleasant and warm in the mountains. If you plan to finish in late September, be aware that the weather is quite unpredictable. If you finish in October, all bets are off. Speaking as a Washingtonian, I'd say unequivocally that September / early October are generally my favorite months to hike, no bugs, great change in colors, nobody really out there. I'd also argue that Stevens Pass north is one of the most spectacular sections of trail along the entire PCT.
Also, any plans on carrying gloves or mittens?
Finally, I carried the same headlamp - great for camp, worthless for night hiking in my opinion. If you plan or have to do night hiking (for example, to get to a post office where a food drop is located), there are many better choices. The e+Lite doesn't throw much of a beam, and i found I was sloooow hiking with it. Of course, by going light perhaps you won't need to hike with it.