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I would suggest cloning the OS install. Install the OS on the 80GB SSD with the Foxconn board that is giving you troubles with the 40GB SSD. Then clone the drives and swap SSDs. WHS 2011 probably will throw up a flag stating that it needs to be reactivated because of hardware changes, but it should go smoothly.
You did not indicate that the 40 Gb hard drive had Windows installed on it and whether it was the original hard disk for this computer.
There is a possibility the 40Gb hard drive is faulty.
Try installing the 40Gb hard drive as a slave drive with the 80Gb drive as the master drive (don't forget to set the jumper on the 40Gb hard drive as Slave. Check the BIOS to see if it detects the 40Gb hard drive, and when the computer boots up, if it can see the 40Gb hard drive and opens the various folders and files, then the hard drive is OK.
You can upgrade the hard drive to a bigger one just as long as it's the
same physical size as the original one. The 40GB PS3 is technically
capable of backwards compatibility. It's just that Sony's OS doesn't
support it on that model (maybe, there will be a firmware update that
will allow it in the future). If you install Linux on the PS3 (which
Sony officially allows you to do), then you can install the PS1
emulator (it's called ePSXe) and the PS2 emulator (it's called PCSX2).
Both of them are free to download for Linux. The only thing that won't
make the 40GB model the same as the 80GB is the finish of the console,
lack of built-in memory card reader, lack of built-in WiFi, and only 2
USB ports. But those aren't neccesary.
Your board specifications are here - http://www.msicomputer.com/product/p_spec.asp?model=661FM3-L&class=mb
This sounds like a memory timing issue based on the caution from the MSI page. There is no reason the board itself should have a problem with that size hard drive. Have you reset the bios to factory default and tried the various compatibility settings available in the bios?