Do you have alarms or anything of sort? (it might matter)
Disable all syncs, try to off (most) of those chat apps like wechat and line etc(go to settings>apps force stop), wechat in particular drains quite a lot.
I don't use stock but mine is close to it but I deleted lots of bloats from TB.
I only leave whatsapp on.
Infact, try out using Airplane, if even in airplane the battery still sucks, try reflashing everything using bootloader.
Device Name: Nexus 5
ROM: Rastakat(all variants)/ Velocity
Other Device: Nexus S/ Nexus Prime/ Nexus 7/ Nexus 10
Devices I meddled with(rough chronological order):
Google Nexus 7(2012), Google Nexus Prime(my new daily), Google Nexus 5(my girlfriend), Google Nexus 4(Sold), Google Nexus S(for everything else), Samsung Galaxy Note(sold), LG Optimus 4X(sold), HTC Sensation XE Pyramid(sold), Samsung Galaxy Wonder(sold)