Based on your answer to my question your console isn't actually overheating. If it was overheating it would beep 3 times, turn on the red light and shut itself down.
As far as why the fan is running high, there are several things that might be causing that...it could be that it's plugged with dust (this does not sound likely since you said you opened it up...I'm assuming you cleaned it while you had it opened). It could also be that you are playing larger games that take up more memory and have intense graphics...this can make the console run hotter and therefore turn the fan on higher.
Unless it's causing some other problem I wouldn't worry about the higher fan speed.
Interestingly Sonys newest model of PS4 the CUH-1200 runs quieter than any of the previous 2 versions.
I hope this helps.