Good idea. Well if you need any help choosing the parts- you can probably start in general computer related discussion, we'de be glad to offer assistance.
As far as cooling- yeah I don't know why it would show that for your CPU temp. It might be that speedfan is reading your motherboard temperature.
With your heatsink fan on, the warmth from the heatsink would be excellerated around the case via the fan. This would theoretically increase motherboard temperature.
But with your heatsink fan turned off, the warmth from the heatsink would remain in and around the heatsink vacinity. This would probably mean lower motherboard temperatures.
My bets are that either your speed fan is reporting innacurate temperatures, or your speedfan is reporting motherboard temperature as CPU temperature.
In any event, it is probably a lot safer to leave your CPU fan on.
When you build your next system, temps may be accurate, but they also may not be. If you end up not trusting your temperatures from the system, you can always pick up an external temperature monitoring device.
I think SSS mentioned a DigiDock. I have this in my main rig. It mounts in your 5.25inch bay and reads temperatures no matter if your computer is in DOS, Windows, or your BIOS setup (since it detects temperatures independant from your system). It comes with several temperature diodes and several fan cables (the digidock can also control fan speed of several fans based on your custom temperature settings).
Ok... I've typed way more than I should have. If you skipped over this, I don't blame you
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Anyway, welcome to the forums!!!