The Denon has the same THD as my existing Onkyo (0.08%). Maybe that is good enough; maybe the very low distortion of the NAD makes an audible difference. That's something I should look into further. The two channel Denon unit is half the price, has the streamer. Not sure if Audyssey is available as an option with the two channel unit.
The Denon, without fretting over an external amp or DAC(while limiting yourself to 2 channels only) provides a signal with .004% SINAD. Also gives you the ability to use a center channel if you'd like, for TV/movies, which is drastically beneficial compared to relying on a phantom image that only works when dead center.
It has all the functionality for high fidelity: bass management, speaker eq, sub eq. It will probably be cheaper than attempting to cobble together a convoluted system of various amps, preamps, DAC's, eq solutions etc that lack the basic functionality of the Denon.
If you want to chase better numbers on paper(i.e. lower SINAD), and dump more power into the KEF's than they can handle(which the Denon can already do), you could add an external amp to potentially increase SINAD to -97 dB(.001%). This way, your speakers at modest volume will produce .501% distortion rather than .504% distortion using the Denon's internal amp/DAC. This assumes keeping the volume rather low...speaker distortion will be much higher in most cases as you turn up the volume.
If the goal is high fidelity, a pair of good speakers along with a pair of good subs will be much better than any pair of speakers without subs within a reasonable price range(or perhaps any price). This is because subs can be placed where they need to be for improved frequency response i.e. eliminating nulls; speakers cannot as you are constrained to where they need to go for imaging.
Essentially, if you want to put a system together that has the potential for the highest fidelity....the framework must include dual subs, bass management, speaker eq, and sub eq. Without these essentials, fidelity will be compromised.
Edit: You are using a PC so will have all this capability!
An idea:
Denon X3700 $800-$1200
Revel F35 $1200....M105/M106 if bookshelves and stands are preferred.
Rythmik L12 pair $1070(can go bigger and/or ported if you want, depending on needs)
Total $3470
Room in the budget for a center channel and streamer if you'd like.
I'd add a Umik-1 mic if you don't have it for $100 that will allow optimal placement of subs and perhaps even speakers if you have placement flexibility.
Edit: looks like you just made a decision. PC based gives you a lot of control, didn't realize this was a desktop system, so most of my post probably doesn't apply, oh well. Figure I'll leave it all typed out just for another perspective if nothing else.
The R3's seem like pretty amazing speakers!
Also remember, subs aren't just about improving extension, but also about improving sound quality no matter how low speakers play. My towers play to 25 Hz in my room but they are very significantly better with subs. I would take bookshelf version of my towers with subs long before I would downgrade to my towers without subs. Even though I hate bookshelves on stands.