ADC Interrupts not working

Southpark:
Also..... could you please explain what this line in your code is meant to do?.....

while (i0 < 1000 || i1 < 1000);

To wait until the sample arrays become full.

Southpark:
Have you searched for material related to adc and due?

Like ... Playing With Analog to Digital Converter on Arduino Due · Nice Circuits - Electronics, 3d printing and robots

Also, the lines in that particular section are all commented out .... by the symbols //
Why is a significant portion of the code commented out?

I haven't found any example where the DAC is triggered by the timer counter, I need the timer counter to generate the desired sampling rate.

There are some lines commented because I'm debugging the code.