if your looking for a good and silent method of moving air through your case in big amounts go for a dual tangential fan mod. one in the lower front takin in and two in the upper back.
these baybies are really quiet and move tremendous amounts of air. i didn´t do it with my own case ´cause of the costs and i don´t mind noisy fans. since i´ve removed the standard fan grills of my case the whistling sound of air through little holes has gone.besides, my ears are already damaged from several punk concerts and big loud drum´n´bass events ;D.
if you don´t cut a window, but a shape (like my amd logo) i recommend using textured plexi glass (or i you like to call it lexan) because it spreads the light better for not having a look-through but neon-sign effect.
back to the cables, and my experiences with ´em : i´ve rounded my cables myself (cut into 5-wire sections, put together and packaged with clear spiral wrap) and it didn´t affect my performance in real-live and benchmarks, but i think it did it´s part in raising the cooling performance in my entire system --> optimizing means to REMOVE ALL "BOTTLENECKS" !