Im going to be honest with you. ive read the entire thread, and some places.. eh.
The 6600e conroe is a great chip, but doesnt overclock as great as the 6300/6400. sure, the 6600e has more cache, btu when the 6300e is overclocked, the performance is neck to neck with an 6600e overclocked. Just trying to save you the extra buck. then, with your cooling, id pick the Scythe Ninja over the Big Typhoon, only being because the scythe has better performance over the BT, about 2-3º i hear. Also, the BT will first give you problems out of the box, because Thermaltake does a terrible finish on the big typhoon, and you most likely will have to lap the sucker before you get to use it.
Thats just my 2 cents. =)
(Ninja, if you give me specs to all three of those modules, i can gladly help you as well.
Also, on the hard drives, i wouldnt go WD on this one, and id have to say spend the extra money on Perpendicular Recording drives (Seagate 7200.10) and put them in a raid setting for maximum performance.