Yes, I did build this myself. The fans are facing the directions that thermaltake recommends. This crazy system has ran for over a year and has done me pretty well. It sits in the open and not near any heat sources. The CPU temp right now is 44C. Oh yeah, I know about the thermal compound too.
What makes me think it's not an overheating problem is when I changed to a larger heatsink and fan, it would shut off during boot. I think I"ve been over the obvioius, ie. fans, cable routing and so forth. Looks like I'll just take it apart and test each component....there goes the weekend.
Oh, if anyone is interested here it is http://www.marroon.com/geek.jpg