1. Good choice on the case, although you may be able to get a different case which is better and cheaper (the BQE is by no means the best). Read this article
for other recommendations.
2. Good choice for quality motherboard, bad choice for reducing heat power. You talk about underclocking, but I can tell you straight that undervolting does a LOT more to reduce heat output (and power draw) than underclocking. Unfortunately, Asus boards have almost never allowed the user to undervolt. I also can't readily recommend a 939 alternative right now.
3. I don't quite follow how lower latency means reduced heatoutput. In any event, I don't think heat is a serious problem for RAM when run at stock frequencies or below.
4. You can't run a computer without a graphics card. Presumably you'll be reusing an older one. Any idea which one?
5. Spinpoints are the #1 recommended. Seagates and Hitachis come after that if you need more space.
6. You may or may not wish to consider a different power supply. The BQE supply is adequate, but hardly the quietest on the market.
And WELCOME TO SPCR