i think disabling it would be enuff,for fan i would run them fast as you can go without it being audible or annoying,its down to personal choice really,i like a nice quiet pc so i go for fans that hit 1600rpm max any higher than that and they start to become too loud,for cpu fan you can set the upper and lower rpm limit in easytune,just adjust the fan sliders and percentage to suite

if the system was assembled for you chances are they would have used cheapish thermal paste,its an easy job to remove the cpu watercooler head just undo the screws and wipe off the thermal paste with alcahol and re-apply some good quality paste like tuniq mx2 or tx3,apply it so the metal cpu base is just covered without showing through and apply as thinly as you can,then screw down the cooler head but dont overtighten

heres my temps/fan speed at idle just for a reference