I got my Music-PC back up and running this tuesday. I'm now using an ASUS E35M1-M motherboard (AMD Fusion E350, just like before). The MSI board could not be replaced.
Getting a cabinet that could take a uATX sized board (The Asus board is a uATX board), and not just a micro-ITX board has turned out to be a pretty smart move, in hindsight.
The board runs fanless, so the PC is even quieter now
The Rega DAC sounds exceptional with Coaxial input: The music sounds far better than the Optical input it was getting from the WDTV, or the USB input I gave it from my HP Ultraportable while waiting for the motherboard replacement.
The DAC has run in nicely now -- I've put about 120 hours on it so far. This may sound a bit cliched, but it sounds even better now than it did right out of the box, especially in the higher frequencies: They are much smoother now, with zero graininess.
I have been playing with the Rega DAC's filters and now I can (kind of) make out what the filters do. Filter 4 (Linear Phase Apodising Filter) sounds best to me. This filter throws the deepest soundstage with maximum separation between instruments, and has a nicely balanced & smooth high-end. The bass sounds the best with this filter engaged -- filter 1, which I used the most initially, is a little too "bassy".
I'll write about the differences in the filters soon.