1.) I have never shorted/bridged the GND & RESET on my Arduino Due 2009.. I have always removed the chip..and treated it as a passive/pass-through type device.. (instead of programming the chip in the Arduino Due 2009. I remove it.. and it uploads the sketch to the blank/custom/standalone board.
If you do NOT have DTR on your standalone circuit.. do as I outline above.. hit the reset BUTTON you have added.. when the text/size at bottom of Arduino IDE displays..
if you are programming the REAL board instead of the blank/standalone.. you dont have things hooked up correctly..
Arduino >>> Standalone
RX >>> RX
TX >>> TX
GND >>> GND
5v+ >>> 5v+
when you hit upload in the IDE... wait for text/size to display at bottom.. then hit reset button on standalone circuit..