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and you might want to check out this
http://www.xoxide.com/computer-cooling.html
The Fan on the very top that blows direclty up...if i cover that it up drastically reduces noise.
1- Should i just keep the Fan on the very top blocked
2-Should i keep the magnetic door closed? and will that hurt my fans?
Get a slower fan or fan controller for the top. That fan does a great job of getting hot air out of the case, blocking it off or unplugging it is a bad idea. 1000 RPM on a good 120mm fan should move plenty of air and be very quiet.