I mostly run my (3)NF-F12, (1)NF-P12 and (1)NF-P14 in 5v alternatively PWM bare-minimum speeds. At full speeds, I've heard no rumbling (I think, we may define the word differently), not from my Noctua fans nor my single Gentle Typhoon I still have as exhaust (which by far is the fan I hear the most when at 1450 RPM)
I'm not a fan (hah!) of the NF-S12 (Not tried NF-S12A), but I'd personally run NF-F12 for air flow as well.
EDIT: My Internet went out due to a storm, didn't notice further replies.
As for cooler, I'd opt for the Silver Arrow SB-Extreme or Phanteks dual tower (PH-TC14PE) if you are going for a high-end tower heatsink today.NH-D14 not long after.
Ideally, you'd use NF-A15-fans on the cooler no matter which you choose