@Andrew: I've never felt the bivy makes a good groundsheet if I'm not inside it. I end up in the dirt.
@John: My Summerlite has been the perfect 3 season Sierra bag for me so far. Wearing all my clothing, I can go below freezing. Combined with the bivy, even lower. As for the Jam2, I have one of the originals (about 5 years old), before they added all the crap (hip pockets, mesh padding on the back, etc). Mine is completely stock at 21 ounces. I don't believe Ursacks are allowed on the JMT.
@Konrad: I like the balaclava- usually wear it rolled up as a beanie. It's a pretty thin OR model. I only wear it as a balaclava for sleep and for cold morning hiking. I really only carry it because it's the same weight as most beanies but a wee bit more versatile. As for long johns, etc., I usually carry cap 1 tops and bottoms, but I'm trying to go lighter on this trip. As I'll be moving all day, I'm not worried about staying warm then- the windshell will be enough and my shirt is a long sleeve. At night, I'll be fine wearing the windshell over everything to bed, including the thermawrap. Keep in mind I also have a bivy. I realized I forgot to add sleep socks though...
@Greg: I've found I don't like the minimal coverage of small tarps/poncho tarps in the Sierra- I've been really screwed up there before. You have to pitch a poncho tarp so low to get full protection that you can't even sit up to cook and hang out. I got stuck in days of storms one summer with a tiny tarp. No thanks, I'll go with something with more coverage that I can sit up under to cook. I usually only use my poncho tarp in the southwest. So why add a bivy to a decent sized tarp? Mainly to boost my bag rating, cut wind, and reduce the chance of spray in really bad weather. I could probably do without since I'm carrying a SpinnTwinn, but I do feel they add a lot of versatility for a small weight penalty. Since I'll be trying to do 30+ miles a day, I might not be able to be too choosy about my sleeping sites; the bivy adds bomber protection above treeline. For 16 ounces, it might be one of the most versatile shelter systems out there; tarp only (great for light rain/wind and warmer temps), tarp+bivy (great when it's getting ugly), or bivy only (great when it's windy, cold, and sites are rocky/small, but skies are dry).