1. Motherboard Vs. discrete soundcard? If the Mobo has Optical out and supports Dolby Home Theatre/Dolby headphone, or any virtualised surround then yes you'll be able to output the 2ch PCM signal to your external DAC. They all do it. Dolby Home Theatre is the improved version (more customisable) of DH as you'll know and is featured with the Xonar Phoebus Sound Card. Of course check this, but if anything can output analog it'll do the same via SPDIF with the same DSP's, EQ control etc.
2. Soundcard PCI Vs. PCI-E? Always PCI-E, as PCI (the longer slot) is being phased out.
3. FiiO D3 Vs. amping the analog outs from sound card? Best left to others - D3 is meant to be very good but your mobo may be just as good. Double amping I'm told req's a clean, low gain and low distortion amp.
4. Which CPU platform should I go with, and what's a decent motherboard for it? Go Intel. It's the cookie cutter/no brainer goto choice. That is if you're gaming on it - otherwise stick to your spec.
Seriously...I have the 3570K (more expensive) and easily overclocked it to 4.2 ghz. Using my Asus P8Z77's included AI Suite software it was a doddle to overclock (though I went into the BIOS to do it in the end). The cheapest Gigabyte or Asus Mobo's will be perfectly fine. Maybe go for the replacement Intel CPU i5-4670K - same price. As for future upgrading.. well I'm happy my Asus will have a decent shelf life. . You only need max 8gB of ram for everything bar photo editing and other stuff.. games atm only use 4gb so 8gb is ideally where you want to be. All your component choices are good. EDIT - lol/.## you just had to be into photo-editing.
Hopefully others can weigh in on this. Point 4 is beyond argument for gaming - sorry all you AMD fans.
Edited by SaLX - 12/7/13 at 3:50am