I'm using a custom rom as you can see in my signature and my battery life is quite good and I have many apps installed. It takes any rom a while to settle down. I can't speak to stock rom because I haven't run stock in over a year. It sounds like you are doing the right things though...pay attention to whatever might be syncing in the background...that can be a big battery drain.
Transformer Infinity 32Gb - JB 4.1.1
ROM: CROMI v4.4 with _that kernel
Nexus 7 32Gb - JB 4.2.2
ROM: between sparksco's sabremod and sbdags' CROMi with M-kernel
SGS2 Epic 4G Touch - JB 4.2.2
ROM: Evervolv, Baked or Magical Unicorn
Xoom WiFi - JB 4.2.1
ROM: EOS 4 Wingray Nightly 180
Rockin' TWRP Touch Recovery
--helps you, give them a THANKS!