If there is overvoltage to the CPU board, you are looking in the wrong place. You want to look at the regulated voltages, not the unregulated voltages.
The CPU receives only regulated 5V from the SDB board. The 5V regulator on that board (Q20) might be having a problem. First - have you done the power and ground modifications to your SDB board?
First read paragraph 4.7.5 here:
Does the Alltek board have a test point for the +5V line? If so, what does it measure (before and after overvoltage indication)?
Easy to guess at the after reading but just want to make sure.
And out of curiosity, measure the 12V (unregulated) input to the Alltek board as well.