Originally Posted by Jedi Mind Trick
You could try speedfan (if you have not already), otherwise, can you manually set fan speeds in the bios? If neither of those work (for your non-GPU fans; MSI afterburner should definitely work for the GPU), you can look for a fan controller/low-noise adapters (something like what Noctua includes with the coolers, which [iirc] reduces the voltage supplied to the fan).
I actually have my nh-d15 low noise adapters sitting in the box lol, but that's just a band-aid, not a fix. wouldn't matter for the gpu either