Most of this is personal opinion, but this is my $0.02:
I would take the Spirit 28, but acknowledge that you might get a little chilly, and might want to sleep lower, and pick sheltered campsites if that is the case. You'll be in a bivy (which will limit drafts), and (can be) underneath a tarp, which will limit condensation on the quilt/bivy via radiative cooling. Note that if you sleep in any of the popular lake basins, it can get much colder than the forecast, particularly if it is a still night. Cold air really does sink. But I'd react to this dynamically, and if you find yourself getting chilly at night, use site selection as a tool to mitigate it. For what it's worth, I've used an Enlightened Equipment 30 degree quilt for the last few years in the Sierra in summer and fall, and been sufficiently warm.
I would bring the gloves. I don't mind chilly hands, but once they get too cold to function, things can quickly get interesting. I don't think I've ever not brought gloves on my Sierra trips, and I think I've used them every time.
I don't know much about the MLD balaclava. I usually bring a fleece beanie, but I also usually have a hooded down jacket, which I don't always use this time of year. I did google the balaclava, and it seems like it might not be a pleasure to hike in, because it looks like it might obstruct vision. At least, it looks like it did for the giddy girl with the orthodontics in the photo that I found.
For daytime hiking, your garb sounds fine, assuming you have a rain shell to cover those arms in inclement weather.
Long sleeved silk underwear is perfect for sleeping in. I've started leaving mine at home if I know I have a good forecast, but you're going to be out long enough that the forecast won't be reliable. I'd bring it.
If you post a full gear list, I (and many others on here) would be happy to advise further–some of us have plenty of experience in the Sierra (but perhaps none elsewhere!).