Since you're using a tarp and bivy, and carrying long-john baselayer tops and bottoms, your 40 degree bag may be fine. I went in Aug 2012 when we had a lot of rain. hail and bad weather and I had tarp/bivy set up and a 30 degree down quilt,(katabatic Gear Palisade) and I was plenty warm. I did not take base layer bottoms, the only long pants I had were my wind/rain pants and I honestly don't remember if I ever slept with them, which I would have if I were cold. For me, in the summer, even at altitude i've found that i don't need long baselayer bottoms if I have my wind pants.
My bottom clothing was just hike shorts for hiking, run shorts for sleeping, lounging, swimming & whatever and my Montbell stretch wind pants for rain. Top clothing was a Columbia L/S hike shirt for hiking, which is sun and wind resistent, a synthetic shortsleeve shirt, a Capilene 2 L/S and my Montane Minimus Rain Jacket. I also had three pairs of socks, two for hiking and one for sleeping, I probably could have gotten by with only 2 total, a sun hat for hiking and a lightweight sleep beenie.
I found this combination to be versatile to mix and match for any conditions from very hot to very cold and raining/snowing/hailing. I really did not need the short sleeve synthetic top, but i bought it in town when the airline lost my pack for a few days, so that's why i had that.
Unless you are very sensitive to cold, it may not be necessary to go hog wild with bringing too many layers, or thick garments. I'm from Hawaii and honestly, I was always fine. if it were raining or snowing during the day, I was plenty warm with my rain gear on and in the evening at camp or at night even below freezing, I just put on all my clothes as needed and i was fine.
The only thing I forgot and wished i had would be a lightweight pair of gloves. I would suggest looking at the Gear Lists forum to see what other JMT hikers had the past few years.