Possibly last set of Q’s to complete gearlist

Since I don't have experience with or opinions of all the points you mentioned I'll just address three of them:

"3. I am on the fence on a wind shirt."
Personally I regard a windshirt as the single most useful piece of clothing I have. Modern fabrics have made some of them so light that they really do seem practically weightless, but even a more robust and heavier model is worth having. If nothing else, you'll appreciate the additional warmth while you're erecting your shelter: it'll make a surprising difference on top of your Icebreaker. I avoid donning my waterproof unless things really get bad because a windshirt handles a lot of showers more comfortably.

"4. Any suggestions on a watch?"
Not a specific model, but I like the more basic Casio digital models. Nothing too fancy: I don't pay more than £20 and I'm interested in timekeeping and water resistance over electronic compasses and the like. If you live near a jeweller's I'd suggest asking them to let you compare the alarms on a few models.

"5. Pants."
As mentioned in another recent thread I'm very happy with the Rail Riders Eco-Mesh and Weatherpants I've had for about ten years. Some details look to have changed on the current models so I can't speak with authority on those, but the Eco-Mesh in particular have been remarkably tough, comfortable and versatile. The only fault I found is the lack of a belt loop at the rear centre of the trousers, causing them to sag uncomfortably below my belt: I solved it by sewing a loop on made from a fabric sample included in a Hilleberg catalogue :) No problems since then.

1. Ground cloth. I've been using the same polycro ground cloth from Gossamer Gear for several years. Cheap and very light.

2. Down jacket. Yes, you can "just use your bag." But I find that to be somewhat limiting when I am trying to do camp chores, eat, etc. So I bring a light down jacket.

3. Agreed with above poster on utility of wind shirt. Think about having to go answer the call of nature at night, in the rain, when you are using your only outerwear as a shelter. Also, on cool, windy, sunny mornings, I would not want to wear my silnylon cape over my base layer to hike. Ick. I love my wind shirt.

Can't help on the rest, sorry.

After reading the reader reviews on the gossamer cloth I think I will just tack one of those on to my order.

I think I will purchase a wind shirt and hold off on a down jacket until aprox. a month before hand and if it looks colder than average I will purchase one.

I didn't see where and for how long you're heading out? You won't need an alarm, I can be almost sure about that.

Aquamira drops as far as chemicals go. They're a little bit expensive, but are easy to use, don't have much of a taste and after treatment, the wait time is minimal.

I mentioned JMT but not that it will be 15 days.

Personally, I don't like wool tops for summer hiking. Too hot and sweaty – yes even the best stuff (Icebreaker, smartwool.)
You might consider something long sleeved, nylon, thin and loose-fitting that will keep both the sun and bugs off you instead.

1. A 2-mil painters plastic will likely hold up for 2-3 weeks, a 1-mil will not.

2. The montbell UL is almost the perfect weight for a chill summer's night at 10000 ft. Using your bag is awkward at best unless you've got a JRB no sniveler or sierra sniveler.

3. I echo what Ray said. A windshirt is a great option for the JMT, especially if you're sleeping in your raingear, and will really boost the warmth of other layers.

4. I have a cheap women's timex digital. It cost around $20, has alarm and some other stuff. It was the lightest watch I could find.

6. Bring some aqua mira transferred to small BPL dropper bottles. Keep the batteries or your steripen in your pocket or sleeping bag overnight or if temps are <40F.

7. Check with the rangers before you leave. We've had restrictions on open fires in many wilderness areas due to fire danger in recent years, and a wood stove isn't considered a stove by most rangers.