This is meant to install the stock kernel(which most custom ROM uses) before you install elementalX, as it could cause problem if you flash elementalX on top of a custom kernel(like franco kernel). If you could find the stock kernel you can just flash it before flashing elementalX instead of dirty flashing your whole ROM.
Letting the battery drain to
almost empty is dangerous and damaging to lithium ion batteries. You should only drain it till the low battery notification pops up(around 20%). Frequent 10%, 20%,50% charging/discharging cycle is good with Li-ion battery,frequently letting it drain to <10% then charge them back to 100% produces a lot of heat in the charging process and is bad for it.