Given that your bag is minimal for the JMT, I would seriously consider getting an 8 oz UL hooded down jacket. I think it would give you a bit more comfort margin. I love (synthetic) vests for hiking insulation, but a much more efficient use of the given weight of down would be such a jacket. The thing about the sierra is that at altitude and low humidity the temperature can really plummet when the sun goes down. If you are tired and drained (as you will be at times) you will find you need a lot more insulation to keep warm than maybe you would ordinarily expect. Also sleeping well makes a big difference on a longish trip.
Marmot Essence rain pants are 6 oz (on my modded ones 5). Since you have a poncho, the number one use of these will probably be as wind pants. I'm actually using these (and a zpacks poncho groundsheet) this summer.
Basically its a pretty good list.
One issue with the 1/8 pad is that picks up and holds stuff from the ground, so use as a sit pad may not work out so great. Better a piece of a ridge rest. You might be able to work out some other protection for the bag by using clothes, or do what other have done and reinforce the cuben on the inside of the pack near the cross-bar with duct tape or tenacious tape.
I will be getting on the JMT this year probably around the time you are leaving it.