I, too, don't have a lot of experience in the Sierras. But, that's ok, they will still let you (and me) on the trail. : )
You have a good clothing system above, even if you take every piece listed. You have the ability to carry maybe 8-16 oz less with judicious choosing. However -- carrying that 8-16 oz won't ruin your trip, as long as you've given careful consideration to what works for YOUR JMT trip, i.e., are you going to speedhike it less than 10 days? Are you going to take 3 weeks or more? Are you going to take lots of side trips up peaks? Are you going to carry a heavy camera set-up that needs to be offset by less ounces somewhere else?
(1) I wouldn't spend $250 for 2 oz unless it is a jacket that you want to have for other hikes down the road, not just for the JMT. I would spend $15 on a DriDucks/FToggs jacket, however. If it rips, who cares? If it sits in the bottom of your pack the whole trip, who cares?
(2) If you choose the windshell pants, you do already have the Arc'Teryx tights as insulation. The shorts-tights-windpants would be a good system and should give you adequate rain protection. The difference between my favorite hiking shorts right now and my favorite hiking pants is about 3-4 ounces, so not anything to get to worried about. Just choose a system of layers that gives you a rotation of pieces that will protect you from sun and rain, allow you to swim if you want, and give you something to put on in camp if you have been caught in a storm (sleeping quilt draped over your bare legs will work here too!).
(3) I carry my windshirt and rain jacket on most trips and I would do so on the JMT without thinking about it. You do see some CA folks here on BPL using just one jacket for both windshell and rainshell, but I think that is often in places other than the high Sierra or on short trips. I think CA is just a place where that is possible.
(4) A lot of jackets: I wouldn't take just a insulated vest into the mountains on a 2-3 week hike. It doesn't seem enough and the weight differences just aren't that great to chance it. Your Alpine Light lists at 12.2 oz (MB's site). You could go with a UL Down Parka (8.3 oz) but you'd have to spend $175 to save a few ounces and have a nearly similar (in function!) jacket. You already said you run cold, so it doesn't seem worth it.
My take-away message: trust yourself, you've already got a great kit to pick-and-choose from. Maybe buy a Driducks jacket just to have in your arsenal of jackets.