OK, so a couple of things come to mind...
The 6502 CPU is removed from the 8032 and plugged into the SuperPET board. There is then a ribbon-cable that connects the SuperPET to the vacated 6502 CPU socket. Examine this ribbon cable and the connectors with a bright light and magnifying glass and 'bell it out' with a multimeter. Check for signs of damage and/or intermittent connection and/or strands of wire shorting from pin to pin.
Next would be to plug together the SuperPET as per the documentation and set the switch to 6502 CPU. Can you configure your 3-board set without the memory board?
Next, check the voltages from the three (yes 3) +5V regulators on board the SuperPET.
VR1 and VR2 provide voltage for the logic chips on the SuperPET. You can measure the DC voltage across C20 (VR1) and C6 (VR2). Check the voltage from VR3 at pin 8 of U3 (the 6502 CPU). VR3 is used as a very crude means of disabling the 6502 CPU when the 6809 CPU is running. All of the measurements should be taken with reference to 0V/GND.
I would set your multimeter to read (say) full-scale 10V DC to start with. You should read from +4.75V DC to +5.25V DC. The closer to +5V DC, the better.
If your multimeter has a low voltage AC voltage range, set it to the lowest range and measure at the same three (3) points again. This time we are attempting to see how much AC 'noise' is present. This may be the limiting factor if you have a relatively 'cheap' 'electricians' multimeter.
See how that goes first... Post the results back.
Dave