Did you experiment with your fan setup? I'm wondering about what's happening with your two exhaust fans at the top of your case. When they are used as exhaust, I'm worried that they might steal fresh air from your CPU and GPU coolers. The air that gets into the case will want to take the path through your case where it hits the least resistance. I'm wondering if the fresh air might then decide to immediately leave the case through the top exhaust without going through your coolers.
That said, you really have to experiment with this. Using exhaust fans at the top is perhaps still be the best performance when the GPU is under load and heating everything up.
On my PC here, what I found out is that removing all fans from the top and closing the venting there up with tape is the best, but my case here is a traditional ATX mid-tower case, not a cube like yours.