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No, I don't think you'll have any troubles with a dual slot cooler card. A major manufacturer like Foxconn or ASUS would have designed the plan of the board to accomadate Crossfire or big graphics cards. You may lose a PCI slot but everything else will be fine.
 
If you're not going to be overclocking then the box cooler will be fine. If you do want to try your hand at it at a later date then I would recommend either the AC Freezer 7/64 PRO: http://www.newegg.com/Product/Product.aspx?Item=N82E16835186134 (for Intel CPUs) http://www.newegg.com/Product/Product.aspx?Item=N82E16835185125 (for AMD CPUs) or the OCZ Vendetta: http://www.newegg.com/Product/Product.aspx?Item=N82E16835202005
Those two are in my opinion the best price to performance coolers on the available ATM.
 
Well an aftermarket cooler can be quieter depending on how loud the stock one is and which aftermarket you get.
 
The Seagate has a 32MB cache and the Western Digital has a comparably weak 16MB. The difference isn't huge, but there is some. (I remember looking at the specs of drives with 8MB caches) The Seagate is probably faster. Stability, I doubt either would be bad.
 
In your opinion, what cpu should I get if the E8400 isn't available at the moment. I mostly play world of warcraft, type papers with word, and surf the net. Maybe some other games in the future though. Also would like to point out that I'd like to be able to have some anti virus programs and anti spyware programs running in the background and not having me lag while im in game. I hate when i have to stop one to do the other. Very annoying.

I also got a question.

why is http://www.newegg.com/Product/Product.aspx?Item=N82E16819115003
more than http://www.newegg.com/Product/Product.aspx?Item=N82E16819115029

Edit:hmm...I'm not even sure if the motherboard I chose will support a 45nm architecture. I'm kinda leaning towards the E6850. Here it is just in case anyone wants to check it out for themselves.

Edit 2:Nevermind. I suppose it will support the 45nm. My mistake :)

ASUS P5E LGA 775 Intel X38 ATX Intel Motherboard
http://www.newegg.com/Product/Product.aspx?Item=N82E16813131219
 
In your opinion, what cpu should I get if the E8400 isn't available at the moment. I mostly play world of warcraft, type papers with word, and surf the net. Maybe some other games in the future though. Also would like to point out that I'd like to be able to have some anti virus programs and anti spyware programs running in the background and not having me lag while im in game. I hate when i have to stop one to do the other. Very annoying.
Well, if that's all you're going to be doing then I you can afford to go for something slightly less powerful and cheaper than the E8400 without noticing any performance decrease. The E6750 would be fine or an E8200 if you can find one. BTW, your motherboard will support the 45nm CPUs. The E6850 is not worth the extra money over the E6750 IMO. As for why the E6600 is more than the E6750, I'm not entirely sure, I would say that perhaps because the older B2 stepping C2Ds have ceased production but are still in high demand as the E6600 has a more variable multiplier than the E6750 and therefore more overclockable.
 
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