Storage [Q] USB charging difficulties

Nexus 7 2012. CM 11 M2 Grouper, - 3-5 hours use daily - Unit is 20 months old.

Until for the first time while playing a game, allowed the device to attempt recharge while continuing with the game after getting a 14% low Battery warning flash on screen.

Factory Charger and connection cable..(this is a 2100 mA strength charger)

The device went dead despite being connected to a charger.
the device went totally dead as the battery drained completely.
the problem appeared to be that the device stayed on and drained the battery.

Opened up the device and charged the battery with a home-made cable - good to go..(98%)
the process involved using 4 sewing needles inserted into the battery connection and crocodile clips to attach, this ensures that the battery is receiving equal current to each side.
this can be done with any type of standard charger but will take longer. the beauty of using the factory charger is that the recharge will only take 3 hours verses 10 hours for a 500 mA type charger. the chargers stop automatically when the battery is fully charged, this would lead one to deduce that any control circuitry related to battery charge levels is inside the charger.

reconnected battery and assembled the unit.
Followed google instructions and used boot menu to switch off device.
turned on device as normal.
Did a factory data reset and wiped all user information.
Set screen brightness to minimum & set battery % inside the charging icon.
Turned off the wi-fi and nfc and everything that could affect battery life.

the device is showing a charging icon when powered off but the battery is not increasing in charge
the device makes a nice noise when the charger is connected.
the device shows the charging symbol in the status bar
the device is not charging and a computer cannot recognise the device.
the device makes charging noises and indications when connected to the computer
the device is not actually charging at all.
there is no apps that could be using unnecessary power. I have stopped the google play service etc. there is only 3 services running.
the loss of power is continuous, even when powered off the device battery continues to loose power.

I am presuming that there is a short circuit within the power sub assembly that is causing this continuous power loss. My reasoning for this is that the operating system is functioning and capable. A fault within the micro usb could cause the effects mentioned above.

the only possible faults are the micro usb port and or the cable that connects the power sub circuit to the motherboard. the cable runs under the battery and the pins are micro size. (it would take 2 people to properly analyse this cable.)
regardless of my particular fault, the advice that i would seek is in regard to any test that I should do to prove either way which part I need to replace.
is there a way to bypass the micro usb connection and power the device via the cable that connects to the motherboard

I have used many different micro usb leads and chargers. The factory charger and lead will charge other devices.
windows 7, windows 8.1, linux mint and ubuntu 14.04 are the different computer systems that will not recognise the device although they will appear to be charging the device without actually increasing the charge at the battery.
I have not found any other nexus users with a similar problem.
Using a moto g, samsung GT9305i, Samsung 5380i, Samsung 5570, all rooted and custom roms.

I will Bluetooth a ROM to the nexus and attempt installation.
Just to eliminate any doubts that could be related to using the m2 version of CyanogenMod 11