Thanks everyone for all the advice. Turns out the cooler itself was the problem, and getting a replacement sorted everything out.
Longer version: As suggested by multiple people, I got better fans. Particularly, found a great deal locally and got a pair of Corsair Pro ML140 and a Corsair ML120. The airflow on these is insane, specially comparing with the GP-14. In the end I had two ML140 in the front doing intake, one ML120 in the back doing outtake, as well as one GP-12 in the top right above the RT doing outtake as well. Saw no improvement at all.
At this point I was pretty convinced that the cooler itself was the problem, and luckily enough, Amazon started selling them again so I could painlessly get a replacement. The replacement arrived, and I'm finally seeing great temperatures. At load, it outperforms the X61, even though my ambient temp has risen from 23ºC to 27ºC. Success!
NZXT X61 (ambient: 23ºC):
- Idle: 40~45ºC
- Load: 75~80ºC
- Prime95 small FFTs: 90ºC (after 2 hours)
Previous RT (ambient: 23ºC):
- Idle: 55~60ºC
- Load: 90~95ºC
- Prime95 small FFTs: 100ºC+ (I shut it down once it passed 100ºC, which took about 2 minutes)
Current RT (ambient: 27ºC):
- Idle: 45~50ºC
- Load: 70~75ºC
- Prime95 small FFTs: 82ºC (after 2 hours)
- Prime95 small FFTs + Unigine Heaven all ultra/high: 86ºC (after 2 hours)
This is exactly what I expected coming from the X61. Great performance! Thanks again for the help.