I need to use Speedfan to control my 3 pin Noctua CPU fans on my mobo's 4 pin PWM header. I have a similar setup in that it doesn't speed the fan up from 600rpm to 1000rpm until temps go over 60 or something.
As for doing the fan swap. You will notice a drop in cooling performance if you use a slower running fan but it may only be a couple of degrees. Personally I prefer quiet over performance as I can't stand any fan running over 1000rpm.
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