"WM Apache 15 deg bag & Nunatak down parka + pants (for sleeping + mornings"
That combo Seems really hot for sleeping. For camp, just the jacket will do. No need for the down pants.
Once you go into mid July through August, the down jacket won't be necessary either. I'd keep the baselayers if you are going out for longer then an overnighter as I have seen cold bad weather even in July on rare occasions in the Sierra. And in June, as I start hiking at dawn, it was nice to wear for the first hour when things are still cold. It's what I get for camping at 10k+ ft most nights.
As someone who only carries a 5oz sleeping pad, your pad choices seem like a lead weight to me. But its your body, carry what you know from experience that you need. A down jacket and some spare clothes in a stuff sack makes for a very soft pillow. You may not need the pillow when you are carrying the down jacket as you won't be sleeping with it on considering how warm your sleeping bag is.
PLB isn't really needed if you are hiking the popular trails as there will be plenty of other hikers. Space bag won't be needed with your 15Fdeg sleeping bag. 3 Bandanas seems like alot. 1 or 2 should be plenty and thats using one as a headband.
Dump the mag-lite. For a flashlight backup, consider some of those tiny 0.2oz Photon keychain lights. I used one around camp for a week on the JMT when I lost my primary light in a deep fast moving creek (forgot to zip my hipbelt pocket where I had it and bent over to fill my water bottle).
Microspikes aren't usually necessary in late spring in the Sierra. If you time your approach on the high passes so you aren't doing them early morning, the snow will be very soft.
Spare batteries are only necessary if you are going to be out for awhile. I prefer to buy things so they all use the same size battery so you don't need to carry as many spares.
You won't ever need more then 3L of water. 1L or 2L is often enough depending on where you are and the time of the year. I normally carry a 1.5 to 2L bladder with a 1L bottle, but I don't always fill it completely up.