It seems like you are looking at a lot of different things and changing a lot of parts. I'm just not sure I am clear on your text and have some questions of the troubleshooting done so far.

I assume that since you have it on the bench, the aux power supply (final amplification on that board) has been completely ruled out and you have no analog out of the RCA connector on the auxillary sound board, is that correct? What points have you looked at with a scope to check the audio path on the auxillary sound board? Do you have analog out the serial DAC? It would help if we found out where the signal is lost so there is some starting point.