The first thing you have to do is strip the system.
Take out any usb devices not needed,
take out pci cards if they are there.
take out 6gb of ram and try to run it with 2gb
If that all doesn't change anything.
Take the disk with the OS out of your system, and try to install Windows 7 on the other empty disk.
Even though no bad sectors were found, the boot disk might be having a problem.
Make sure in the BIOS PNP OS is set to yes.
Check in the device manager that Windows 7 indeed is installed as ACPI system.
If you did any OC, or set timings for the ram, set them back to default in the BIOS.
You have to exclude possibilities to get to the heart of the problem.
Good luck, and please post back.