i would take a serious look at this possibility. if your case fans aren't set up for optimal cooling, there's a chance that hot air may be building up inside your case. the temperature of the air surrounding your CPU's HSF can heavily affect its ability to cool your CPU. the temperature of the surrounding air should obviously be cooler than the fins on your HSF. the smaller this temperature differential becomes, the less heat your HSF will be able to radiate away from your CPU. if the surrounding air temp eventually becomes equal to the temp of the HSF's fins, no heat will transfer from the HSF to the surrounding air OR vice versa. if the temperature of the surrounding air ever eclipses that of the fins on your HSF, then obviously the HSF will not radiate away the CPU's heat, but rather it will absorb the surrounding air's heat, thus heating your CPU further...not that i've ever seen case temps that high before, but that's how heat transfer generally works in theory.
you currently have 3 intake fans and 1 exhaust fan. without even considering the airflow characteristics of your case, it sounds to me like you're taking in more air than your 1 exhaust fan can evacuate...granted, i know other factors play into a fan's CFM like RPM and the # of blades (and not just the fan's diameter). but all other things being equal, and assuming your top fans are also 120mm, all that cold air being brought into the case may not be getting evacuated quickly enough by the 1 exhaust fan. in other words, if your fans are all approx. the same size, and the 3 intake fans are operating at similar RPM's, then the 1 exhaust fan has to be spinning ~3 times as fast to exhaust the air being brought in by the intake fans. remember, the more time that fresh cool air spends inside the case, the less fresh and cool it stays. you have to find a balance of fans that keeps cool air circulating through the case at a quick enough pace that it doesn't become stagnant and hot inside.
i think your idea of switching the rear fan to an intake fan and the top fans to exhaust fans is worth a try, but only if you can reverse the direction of the flow of the Noctua (or rotate it 180°) so that it isn't fighting against a rear intake fan. i'm pretty sure you can't rotate a Noctua unit 90° so that it blows up or down, but you might be able to rotate it 180° (or at least rotate the fans 180º) so that it flows the other way, that is, from back to front. this way, cool air comes in the back and cools the CPU right away. the Noctua then exhausts heated air toward the front of the case, where the top intake fans suck it up and out.
personally i think your top fans should have been exhaust fans in the first place. after all, hot air rises, so the top of the case is a natural location for exhaust fans. i'm assuming you don't have a place for a fan on the removable side of your case?