I carried the mtn hardwear phantom 15 plus a montbell thermawrap inner jacket. I found that usually I just wanted to crawl in my bag at the end of the day, so camp clothes weren't really necessary. However, my friend and I were pretty typical 19 year olds so we started hiking late every day and slacked, so we were almost always hiking a little into the dark. I slept in the montbell every night it was cold, and it is unbelievably flat at this point which leads me to doubt the longevity of the cocoons, particularly for a trip that long. As was noted, the coldest parts are the start, the sierra, and then northern washington. I wouldn't want to be facing weather in the northern cascades with a compromised sleeping system. If I did it again I'd carry less weight and use a quilt, bivy and tarp combo. One big advantage of the quilt that I was envious of was the vastly increased drying time over a down bag.
Oh, and I think you said you were going to take an atlantis wool hoody, which I would get rid of. A powerstretch shirt would be far lighter for the warmth, and a warm layer for hiking beyond a rain shell was totally unnecessary in my experience.