I would go as CA_Steve suggested, the MSI N760 seems the best of all in terms of noise. In the past i had good experience with Artic Cooling, but not the last time. I was set on getting a gtx780 asap, no custom coolers where avialable and asus directCUII seems to be aimed more for performance than quietness, no other manufacturer had any info on theirs, so i decided to go with Artic Cooling Acelero III, out of having such a good experience with GTX780 galaxy (had that cooler from factory). But there is something wierd with this gen of gpus, specially the gtx780, i can contol the fans, but they go out of contol by themselves, its like something on the gpu dont recognize the rpm of the fans and the gpu ramp it up to max, this behavior happens every 10sec, there is even a thread
where others are experiencing the same as me. I also was lucky to know a friend that just took of a Prolimatech Mk-26, and borrowed me the gpu Y pwm splitter to test other fans, and here is is worst, the fans always run at 12V (tested noctua nf-a14, thermalright ty150 and prolimatech vortex 14). So this tells me there is soemthing not standard on the GTX780 on their design of their pwm. Im not sure if the GTX760 will be the same or not, but for this alone i wouldnt recommend it, just go with MSI N760, and if you find it not good enough for you, then do the Artic Cooling over it.
I also agree with steve, i would use the R3 you already own, or a more quiet oriented case, the Prodigy seems very open with none standard fans, so its a risk. If you want micro atx, there is also silverstone tj08-e and PS07 or fractal define mini.
I would go with Asus for fanXpert2, there are lots of options even beside the gene VI.
If you go into the prodigy M, i woudlnt go fanless, Seasonic X series ask for an horizontal orientation and to be one side, this is the way its design for it to work, in the prodigy M the PSU is horizontal and i dont even think a fan will give it airflow, for this case i would use a PSU that has a fan on it like Seasonic X560 or Kingiwn LPZ 550.
I would avoid if possible a AIO water cooling, specially the small ones, you will also add the pump noise to the setup. I would go with something like Scythe Mugen 3/4 or Thermlaright HR-02.
Slipstreams are fine
I would go with the plain 4670 and avoid the T, the T versions are just underclock from factory nothing special and they also include a low profile cooler. Its like paying more for less.