I think generally you wil find that the stock coolers are fine. Since HTPCs are low power devices, the CPUs run cool and the fans never really need to speed up much (so they don't make a bunch of noise).
I would just try the stock cooler and see how it sounds - no need to order a cooler now.
Regarding the GPU. You said it sped up to 6000 rpm then you pulled it. Did you give it a chance to settle down. My GT440 spins the fan up to full when I first start the computer, then it slows down to (silent) a few seconds later and I never hear it again.
I would just try the stock cooler and see how it sounds - no need to order a cooler now.
Regarding the GPU. You said it sped up to 6000 rpm then you pulled it. Did you give it a chance to settle down. My GT440 spins the fan up to full when I first start the computer, then it slows down to (silent) a few seconds later and I never hear it again.