Issues using E-MU 0404 USB for measurements (ARTA and RMAA)

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The ground lift disconnects the GND line of balanced inputs too? You will need some ground reference. If your EMU PSU and amp PSU have protection earth, you can disconnect the ground lift. If not, IMO you should keep it engaged since it aligns the grounds of the amp and the soundcard and there is no ground loop in your setup (provided your input signal is really galvanically isolated from EMU as shown on your diagram - please check that too).
 
The FX 802 I plan to measure has no ground reference.
It takes the digital signal in and makes a PWM conversion at the final stage (No DAC at all), please see the STA326 data sheet.

In RMAA, the output would be the digital signal and the input the signal from the speaker outputs (after the voltage divider).
 
I do not think your balanced setup will generate good measurements if no relation between EMU ground and the measured output is established. Try it, perhaps it will be OK. IME a relation between the two devices needs to be established, no just via hot and cold lines of the balanced inputs. I would make proper balanced dividers (not just single-ended as in your diagram) and connect the central points ("virtual ground") to the ground terminals of EMU inputs. That link I posted a few days ago https://www.diyaudio.com/forums/pas...ier-distortion-measurement-4.html#post3735528 has all the details.
 
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