Note: It is new version HICTOP main board, it is compatible with 3DP08, 11, 12, 16, 17, 18 etc, but when you use this one you will need to insert the SD card into the card slot on the main board instead of the one on the LCD
When installing Firmware on Stock Controller SD works on the 2004 LCD {RepRap Discount Smart Controller}, When installing Firmware on new controller the Onboard SD Card Reader works and disables the 2004 LCD SD Card Reader.
Now there must be a way around this, a way to swap External for onboard SD Reader Slot.

Schematic of 2004LCD shown below

It appears that the New Controller Circuit is close but wired to different Arduino Pins this means that I can change it.
Will look closer at pins_RAMPS.h section for SD Card Reader, as Both Controllers have the same pin-out for the EXP1 and EXP2 connectors.
Need to find how and where it selects the onboard SD Card Reader in lieu of the External SD Card Reader.

Any help will be appreciated.