I'm on stock but had the same problem. Phone totally discharged, plugged it into my car charger, phone got hot by camera but did not charge. Got home plugged it into stock charger, same thing. Battery charging on screen, phone hot, then dim light on screen. tried for a day or so, no luck.
Tried holding power button for 20-30 seconds, nothing, Vol up and down + power, nothing. By accident held power and vol up and charging light came on, held it for a minute, and it stayed on, let go, out it went. As a last resort, put two rubber bands around the phone to hold in power and Vol up and bingo! Charging light stayed on! left it overnight and found the phone completely charged in the AM, green light flashing. Been working fine for days, Willnot let it get too low of a charge in the future.