I uploaded a new version of the MCU design (minimal changes) to github and dropbox. Commit logs:

• Changed names of SPI signals in DIMM
• Copied in MCU design by O_Shovah
• Repaired MCU design: There were several defective wires: not attached to pins and wrong names

@O_Shovah: You still have some trouble with using eagle. Some of your wires were not connected to the pins they touched. The order is important here: either place a part on top of existing wires or draw a wire to touch a pin. Moving a wire to touch a pin does not work. Also, you cannot change the signal carried by a wire by placing a suitable label close to it. You need to use the NAME command. It is usually a good idea to first use the label command to actually get the name displayed and then use the NAME command to change it and see the change in the label.

I currently placed two MCU supply voltages on the DIMM connector: +5V which is connected to the USB 5V, and +3V3, which is connected to the output of the LDO inside the MSP430 (this LDO is fed by the +5V). I wanted to have the backplane supply 5V only if it used the USB connection and supply 3.3V otherwise. But there should be a different way to detect the presence of the USB host. So any concerns about removing the +3V3 signal from the DIMM?