The intake fan is at the bottom of the front panel near the GPU and the CPU is at the top of the case
In front of the inlet placed at the bottom of the front panel, there's the lower hard drive cage, and there cannot be a GPU (as there are no slots): so, if I don't get you wrong, I think that fan is just above that cage, in the upper-middle of the front panel (as seen in your photos, though). At any rate, maybe you might try to (firmly) place that fan near the GPU, either suspending from the ODD cage or placing onto the HDD one, in order to see whether the GPU temp may lower (at the same current speed, of course), or not (a somewhat rigid support should work probably better than something like zip ties, which otherwise may come handy for a quick and dirty trial).
CPU fan noise and temps aren't an issue at this time.
As I said a while ago with different words, whether you can't hear the crappy Intel stock heatsink, that may mean the rest is somehow noisy, rather than actually quiet: btw, usually CPU temps are figures, not subjective assessments, and those figure may help us to assess whether you may need more heat exhaust prowess or not, much more than stating "aren't an issue at this time".
I have made some attempts since your reply to change the fan curves. The AsRock utility allows for 5 points of control - I couldn't get speedfan to work properly with this mobo
As far as I know, you shouldn't be able to install the ASRock utility and SpeedFan at the same time, without the former mess up the latter's settings: anyway, whether the ASRock utility works to actually lower the Noctua speed, that might be enough.
On the other hand, what SpeedFan might be able to do is to control the ASUS R9 fans also, helping to lower the GPU noise (at the expense of the load temp, though): if I'm not wrong, you can use Afterburner (or any decent Rivatuner derivative), alternatively.