The jitter you are measuring is not the same thing as the clock jitter that was mentioned earlier in the thread and will not affect the accuracy of the ADC readings. Clock jitter is caused by the accuracy of the timing and waveform of the master clock oscillator and there is nothing we can do about that.
The line adc_init(ADC, SystemCoreClock, ADC_FREQ_MAX, ADC_STARTUP_FAST); sets the prescal value - there is also ADC_FREQ_MIN and you can pass any value in between.
It isn't possible to get a buffer per channel as far as I know. There is a tagged mode where the highest 4 bits are written with the channel the sample came from, that is useful when you enable more than one channel.
SerialUSB works as fast as it can, the baud rate is ignored. Since it's USB2.0 the port is faster than the SAM3X can throw data down it. I've had it running at over 50Mbit/sec.