Thanks for going to that effort, I haven't done any testing so all I can say is my battery has been lasting longer the past couple of days than it used to. Maybe there's something specific to your phone preventing a similar experience?
I don't think so. The apps are quite similar to those I used when it was 4.2.2.Also I never installed suspicious apps. Most of apps on my Nexus are from reputable developers and editor's pick.
It would be great if someone perform similar test as mine. I charged to 100% and used to 35% to see Screen On Time. I'm using stock ROM too.
Or turn on airplane mode before bed and see how many % battery was drained during night.