To measure vss voltage on my mpguino, i set my meter to 20vdc, stuck one probe on electrical ground (what you call "12v neg"??), then touched the other probe to the 'inner' side of the resistor. This would be the same as touching the "analog pin 0" contact on the board, where the vss signal goes in. This is where you should see it bounce from 0 to 3v while the wheels spin.
If you're not getting a reading from your VSS wire, with or without the mpguino attached, you must not have the right wire. Your key must be turned to "ignition on" to get any vss signal, but engine probably doesnt need to be running.
Dont know what to tell you about troubleshooting for damage, though. I'm probably fortunate myself, that i havent fried something on mine
