If you didn't apply a good thermal compound between the heak sink and cpu you are likely to cook the cpu rather fast at some point. That conducts the heat from the cpu into the hsf. The 40C is still within a normal temp range while nor being the ideal there. The max temps on most new models both Intel and AMD run about 60-70C.
Increasing the air flow even going with a better case would certainly help see all temps drop lower. Having a large front intake as well as a large rear exhaust fan will see the cooler air drawn in through the front while the heated air gets blown out at the rear of the case.