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 - KK 4.2.2
ROM: CROMBI.KK with _that kernel
Nexus 7 32Gb - KK 4.4.2
Galaxy Note 2 - 4.3
--helps you, give them a THANKS!