here are some thoughts I had. Mostly changes that I made when I was getting ready for last summer (and what I'm doing right now).
1. Even though the weight of the granite gear crown 60 isn't too heavy, it'll be way too much volume for the gear you'll end up carrying. If you haven't already purchased it I would hold off. I had a Gregory 70L pack and I thought I was going to be able to use it but it would have been way too much after I got all my gear worked out.
2. You're carrying pants and shorts. I didn't carry any pants on the JMT section I did this year and it was fine. I just used lightweight running shorts and briefs.
3. I would consider a wind shirt. It's really lightweight, keeps the bugs off, helped me regulate my temps when it was both hot and cold, and the list goes on.
4. You're carrying a down jacket that weighs 14 oz and silk base layers that weigh 6+ oz. Ask yourself when you will be wearing the down jacket...just at night in camp or under your quilt? On the trail in the morning? Can your jacket handle being under your straps while you hike? I have the patagonia nano puff which weighs 9 oz and I brought long john bottoms and I was totally fine. Also keep in mind how warm your quilt is. If you have a 20-30 degree quilt and you're a warm sleeper you might not need all those extra layers.
5. Your stove and fuel weigh app. 15 oz. I would consider checking out the Caldera Keg with the Esbit tabs. My stove, cone, lighter, esbit graham cracker, spoon, carrying sack all weigh 3.6 oz. The tabs weigh about .5 oz each and I used a little less then one per day (I hot meal plus a big cup of hot chocolate each night). I was hesitant at first since I was so used to canister stoves but it's surprisingly easy to use and it looks cool!
6. Your Steripen, batteries and bottle altogether weigh 7.5oz. You should try the Aquamira drops. If you repackage it and have a small mix bottle it'll end up weighing less than 2oz and you won't have to worry about any electronic failures. I originally tried this with tap water at home and I hated the taste but I tried again on the trail and I never noticed it. It's worth a shot.
7. I know some people feel really strongly about hiking in boots and feel that having that ankle coverage/protection is really important, however, I would encourage you to try some trail runners. They are extremely light and will dry a lot quicker as there is a lot of water on the JMT. Give it a try on some day hikes or overnights and see how you feel.
The nice thing about starting your preparation this far out is you have a lot of time to test out gear and get help. This site helped me immensely when I first started (not too long ago) and I still pick up tips all the time. Hope this helped some!