You definitely have a good selection to choose from...hopefully I can give you some additional insight. I did the JMT this past Sept 2011. We got about a weeks worth of rain, light dusting of snow, and 8-10mm hail, and had highs up to 90* and lows around 28-32* in the morning, so pretty extreme for the sierras. Because you are going earlier in the summer, I expect temperatures to be even milder. I carried fairly little clothing...maybe this can serve as a guide.
I wore/brought the following on my trip, which I felt covered the entire temp range of our trip.
From Head to Toe:
*Generic Polartec Fleece Beanie (army surplus)
*A wide brimmed sun hat (REI brand)
* a lightweight wool short sleeve T (Backcountry.com brand)
* a long sleeve silk weight Capilene 1 Jacket (Patagonia)
* a synthetic hooded pullover for insulation (BPL cocoon brand)
* UL rain jacket (marmot essence)
* Lightweight liner gloves (OR PL gloves)
* running shorts (2 pairs of very light shorts, 1 nike, 1 patagonia)
* 200weight Wool Tights (icebreaker)
* wind breaker style pants (Montbell dynamo pants)
* 2 pairs of socks (1 wool darn tough socks, 1 synthetic injinji)
* trail runners (Montrail Mountain Masochist)
After the trip, I determined that I definitely could have changed some things. I could have used a windshirt. The additional 2-3oz would have been worth it to me. The passes were extremely winding (and cold!) as were some of the long stretches of open back country. The rain jacket served as my windshirt, but I wasn't able to wear it as long as I wanted, because I would overheat after a couple hrs. I think the slight weight penalty would have been worth the extra comfort. The wool short sleeve shirt never got used (other than to serve as a pillowcase for my inflatable pillow) simply because I preferred the arm coverage afforded by the long sleeves of my capilene. I carried less sunscreen as a result. I guess the only other time I wore my wool SS shirt was when I did laundry at Reds and VVR. But of course, I could have just worn my rainjacket for modesty if I didn't have the wool SS. Not bringing any underwear was awesome. The liner in my running shorts worked very very well, and bringing 2 running shorts meant I could rotate and wash accordingly. When it was raining or windy/cold, layering a combination of my wool tights, windpants, and running shorts took care of everything. I enjoyed having a mix of injinji and normal socks. The injinjis definitely help prevent blisters, but they aren't very durable. My gf wore a huge heel in her pair after only 2 weeks. The normal wool darn tough sock was much more durable. Also, I vowed to go home and buy a pair of dirty girl gaiters right away after my trip. The extra couple of ounces would have saved me tons of time...I wasted a lot of it, taking off shoes to empty out sand/pebbles etc.
So after reviewing your options, I think you should definitely switch out the softshell gloves for a lightweight pair of liners. Softshell will probably be too warm for time which you are going. Also, light liners provide sufficient warmth, while still allowing use in warmer temps (meaning you can prevent sunburns on your hands) I wore my gloves a lot on this trip. The synthetic nanopuff pullover is a good choice...very similar to my own insulation on the trip. Your cap 3 tights are pretty much the same warmth as my 200wt wool tights, so I think that will be solid.
Definitely leave home the R1, but bring the windshirt. I have a R1, and it only gets brought out for really cold winter trips. A combination of your capilene, nanopuff, windshirt, and/or rainjacket will tackle all conditions. Also, definitely drop the Alpha SL at home....to much jacket for a tame trail/conditions. The dri ducks will be fine.
Do you have a hat to keep the sun off you? I see no mention of your pants. I enjoyed my running shorts/windbreaker pants so much that I will never bring normal "hiking pants" on any of my trips. I'll admit...the temp range was limited though, as I would overheat in my running shorts windpant combo around 85* Which meant that I would have to use my running shorts with a good amount of sunscreen. Not that I'm allergic to sunscreen, or that sunscreen is bad for you...but the good stuff tends to be pretty thick/greasy, and is just plain disgusting to wear to bed without washing off. Imagine dealing with that for many days at a time. Nevertheless, something to consider since you are going during the summer.
Also, no need for a balaclava...it doesn't get that cold. And if you really really wanted to bring something to cover your neck/mouth, bring along a buff because it's more versatile. We had frost condensation that would rain down from my tent on many nights...it was a bit annoying, and a buff would have made things more comfortable (the frost falling on my face would wake me up sometimes), but I did fine without it.
Hope that helps!