I hiked the JMT last August/September as one half of a duo. If you haven't seen it, I have a trip report here, with a full gear list.
Since I can't tell what you already have and what you're purchasing, some of my advice may be referring to non-negotiable items. With that in mind, my $0.02:
1. I'd get a different shelter. Bugs will not be a problem, so no need for anything with netting. Marko gave you some good links above. I'm partial to Zpacks and Mountain Laurel Designs, and would advocate any of their offerings. You haven't made the transition to tarps yet, but again, there will be NO MOSQUITOS on your trip. Get a tarp or shaped tarp that pitches with trekking poles (and take (and learn to use, if necessary) trekking poles--I didn't see those on your gear list).
2. I'd look for a lighter pack, if you can lighten up your base weight by a few pounds. IMO, you've got about an extra pound of pack.
3. Is a Sawyer Mini really 7 oz? A Steripen is 4.6 oz or so, and repackaged Aqua Mira drops weigh only a couple oz. On the topic, I almost always bring repackaged Aqua Mira drops since they weigh so little, as a backup in case my primary fails.
4. Are you both carrying full cook setups? Definitely share the stove and fuel.
5. Is that a L Neoair XLite? The S weighs only 8 oz--half what the L weighs. I made the switch to torso length sleep pads and will never look back. I suggest trying that.
6. I'd bring the zip-off pants section, and leave the rain pants at home. Even in an uncommon multi-day rain event in the Sierra, acknowledge that your shoes, socks and pants will get wet. It's fine. When you get to camp, you'll put on your (dry) socks and long johns, and climb into your (dry) sleeping bag. I would also want those zip-off sections for wind protection--it can get quite cold in the Sierra in September. I (and many others on here) have been snowed on. Also, you'll need less sunblock if you wear your pant legs.
7. I'd leave the mug at home. I use a 20 oz Gatorade bottle as a mug and as a water bottle. It works fine.
8. I'd get a lighter headlamp--in fact, I'd bring three Photon microlights; two white and one red. That comes to 0.75 oz and gives you great redundancy.
9. I'd leave the toothpaste, Dr. Bronners and DEET at home. Bring some floss.
10. I'd consider bringing Erik the Black's trail atlas. It has many campsites and water sources listed. Have one person carry the Tom Harrison maps, and the other the trail atlas.
11. I'd bring the sleep socks (Possum down are great, or down booties for more $$). I like a clean, dry, fuzzy pair when I sleep. Maybe I'm a wuss.
12. I'd bring horse repellent (ah, inside joke--if you read my trip report, you'll get it).
This is all mostly nitpicky and matters of preference--most importantly, have a great time!