Steve,
If you measure the output pins of the 5 volt and 3.3 volt SMPS boards and see a low resistance (~2 ohms) you may have damaged the CPU. I had a similar fault and the CPU and IC402 were destroyed. I sent my QMX to Jeff Moore, who brought it back to life. You might want to make some measurements and contact Jeff and get his feedback.
?
Dennis
KK5DB