The default setting for the power is standby mode @ 30 minutes, every time you clear the bios that's what it's set to.
My next step might be swapping out the hard drive, since it seems like when it restarts the hard drive won't spin back up (and yes, you can tell when a Big-n-slowfoot spins up

). I might also start swapping drive cables to see if I have a weak cable causing weird stuff.
BTW - This has to be the most cramped case that I have ever had to work on!