I can't speak for LTE but I only had deep-sleep issues until I installed Cpuset and moved it to be a system app. Cpuset will eventually start failing unless you move it to be a system app. I clean-flashed 3/16 meaning I formatted absolutely everything except external before flashing.
Recipe:
*Cpuset must be successfully moved to be a system app or it will fail, repeatedly*
100% clean flash 3/16 CM12 w/TWRP Lollipop
(I used Pico GApps, probably doesn't matter)
1600 MHz (default)
interactive governor (default)
deadline scheduler (default)
Good luck!