Why does my DIY Barebones Arduino Due with SAM3x8E overheat on RESET press?
I figured out my mistake the other day, and man was it a stupid one. The chip was soldered in 90deg in the wrong direction. Pin 1 should have been located at the top left. I got confused by the silk screen and the two larger dots, one of which I mistook for being the pin 1 marker. I did not think the orientation was an issue at all until it was pointed out to me. This chip will need to be replaced now most likely. 

UPDATE: 

I flipped the chip 90deg and it WORKS!!!! I haven't tested the full chip, I am sure this must have damaged at-least SOME parts of the chip? Still surprised it even gets recognized. Kudos Atmel!