Well for cooling put a 120mm or 140mm fan in the 5.25 drivebays if you have room, that will help more than anything for temps. The 140mm will just slide in nice and tight, the 120mm you will have to mount it. The noise levels I can't really say, the 2 Scouts that I built where very quiet. Do you have stock fans? If not are you using any fan controlers on them? Is there wires hitting the fan blades? Do you have anything loose in there, maybe a long shot but the back panel can be hard to put on sometimes, did it pop loose before you got the screws in? Do you have fans in the window? I never did that but a lot of people said that they got a lot of fan noise from that.
I wouldn't mind ordering some silent fans to replace the stone ones. Any suggestions on good, quiet fans with red LED?