I have a Sonos and a Parasound zDAC in the bedroom system - far less expensive than the stuff in the big rig, but it's a great combo. In all honesty, with 16/44 material, the difference in sound quality is very subtle. For just under $500, the little zDAC is terrific.The Audio Research is a great DAC. I went from a Theta to Bryston BDA-1 and next BDA-2. There are so many great DAC's out there. Like anyone in this hobby your always wondering what's better.
Interesting about the Marantz. Wonder how the Sony is fairing.
I have a question, do you think your Flac files sound better than the same CD played through your DAC?
I'd expect Sony's Z1ES player to be an excellent device and I'd bet a month's pay that it isn't plagued with the same shortcoming the NA7004 has/had.
I ripped my CDs to WAVE files - don't really care about metadata. I just wanted the files on disk ready for creating my own CDs. Of course, that was an issue a few years ago, but it isn't anymore - have an iPod as a source in my car now (and play straight from thumb-drives in the other vehicles). To answer your question, yes, I honestly think playing the files betters the sound quality of playing the CDs. It's not the DAC - I've routed a digital output from my universal player to the DAC7 for an apples to apples comparison as you mentioned. I take it you made the same observation. It surprised me.