What makes you think the l/r output of the adc is perfectly ballanced to the analog out of the ua5?
It's not...
The analog out is affected by 2 things which DON'T affect the digital output (and can lead to bad readings after you've calibrated
1) monitor switch (on/off, should be off, pain in the butt since it defaults to on)
2) output level (the one above the headphone jack)
And if you accidentally leave the monitor button on, then the monitor volume level becomes the 3rd factor that changes analog output level without affecting digital output level.
So yes, the line-out of the JB3 would be the best place to run the SVU for consistency. The down side is it *might* shorten the JB3 battery life a little bit as the JB3 is now driving an additional load.