Let's see:
GPU is way too hot.
HDDs are hotter than normal.
CPU is hot but that's explainable, CPU fan for some reason is running at variable speed, probably controlled by the MB, if so, disable this, the CPU fan should always be running 100% speed.
I'm puzzled as to why you can't change the direction of the HSF. The freezer pro uses intel's standard push pins for mounting if i'm not mistaken, so it should be able to mount in either direction. It's not like the AMD boards where the retention bracket only allows mounting in one direction.
But I'll tell you what your biggest problem is: your case. You could solve a lot of problems if you switched to a case with a bottom mounted PSU and top exhaust fan, and preferably a decent sized side panel fan to help cool the GPU. With that even if you can't change the direction of your heatsink, it's still blowing the hot air outside the case.