Sorry to hear about your GF, I hope she recovers quickly. That just shows us that there are more important things in life than backpacking. That being said here are my two cents on your list:
Shelter – My only comment is that 12 stakes is quite a few – to you really need that many for “The One”? Also, though groundhogs work well, they are very heavy. I am not saying they aren’t worth it, just giving you something to think about.
Packing – Your pack is pretty heavy. I would shoot for something in the two pound range. With a inflatable pad and a bear canister I would think I lightweight framed pack would work best. Think Gossamer Gear Gorilla or Mariposia Plus, ULA Ohm or Circuit, SMD Swift, Hyperlite Mountain Gear Windrider or others.
I would also add a trash compactor bag liner for waterproofing. (~2.3oz) I know you have the Packa for rain, but what if you slip on a stream crossing?
Hygiene/First Aid “Blue Bag” – What is in the 3oz first aid kit? It seems like you have a lot of meds listed already. I would think about repackaging the Body Glide, Naproxen, and Sunscreen to a week’s portion. I would eliminate the E-stove and space blanket.
Essential Gear – I would drop the phone or the spot. I doubt the cell reception is that good on the JMT so the phone would probably go. Actually with a group, I would probably drop both, especially if someone else has one. (Or you could carry them and let someone else leave them – no need for two) I would drop the Ti Trowel and use a tent stake, etc.
Hydration/Cooking – I think the jetboil is heavy for solo use, but the Ti version is better than older versions. There are lighter stoves out there both canister and alcohol. It is light, but I see a lot of broken LMF sporks, but YMMV. I would drop the filter and use repackaged Aqua Mira.
Packed Clothing – I would drop the LS Shirt (Actually I would wear it instead of the SS shirt for sun protection). I would drop the UA sleeping underwear and just sleep in your long underwear. I would drop the softshell pants. I might hike in pants, but not carry an extra set of “hiking” pants. If you want to stay with the kilt and it turn off cold you can always wear your long underwear underneath for extra warmth. I don’t think you will need the Down Pants. Replace the daypack with a regular stuffsack for stuffsack/pillow. This should run you under an ounce. Save yourself a pound and leave the water shoes at home.
Oh, and by all means, this is a trip of lifetime, take a camera.