This morning was somewhat of a break through with getting the comunication working with the mpu6050. It turns out that the twi2 pins on the due dont have the required pull up resistors to work with the I2c bus installed, and so the channel was constantly low. I then connected the sensor to the TWI1 SDA and SCL ports, which do have internal pull up resistors built in, and ran the I2C scanner code, and it found the device on 0x68. I then tried to run the example code that I got from the arduino play ground, and this worked, outputting values for 6DOF movement.
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