I believe G-SKILL Sniper Series is 42mm tall so no problems there.
NH-U12P SE2 is not as good as suggestions above.
Ninja 3 and HR-02 are both good coolers.
NH-U12S with one fan is only 1c hotter than with 2 fans.
The money saved on cooler could be used to setup case cooling
You may have seen this before... I've posted it many times but as it applied to this discussion I will add it again:Warning: Spoiler! (Click to show)
There is much more to cooling than the CPU. Modern GPU's make more heat than CPU... and getting that heat out of the case can be a challenge.
Setting up the case to cool properly is the hardest and most time consuming part of a build... And the most neglected by most builders.
Putting fans in case as intake and/or exhaust is only the first step. These fans only move air in and out of case.
This does not mean heated air is not mixing with cool air.
Nor does it mean cool air is going to where it is needed.
Getting the air to flow inside of case properly is even more important. We want cool intake air flowing to components and heated air from components flowing out of case without mixing with the cool air and warming it up.
How we manage that is what determines where the air flows inside the case. We can do this several ways; deflectors, cooler intake fans, exhaust fans, removing vent grills, using fans with higher pressure/airflow, building ducts to or from CPU/GPU cooler, etc.
Using a remote temperature sensor to monitor what air temps are is the key to finding out where the cool air is flowing and knowing heated air is not mixing into it. By monitoring this we can than make changes to get airflow the way we want it.
I monitor the temps with a cheap indoor/outdoor wired remote or terrarium digital thermometer. Twist a piece of stiff insulated wire into the last 8" of sensor lead so you can bend it to position sensor where you want it... like 40mm in front of your GPU cooler/radiator intake.. to see what the air temp going into CPU / GPU cooler is compared to room temp. The closer it is to room temp the better.. Shouldn't be more 5c maximum, 2-3c is what I usually end up with after 30 minutes full load on both CPU and GPU.
Warning: Spoiler! (Click to show)