I have $1 on the table that says its a bad connector for the motor.
Under the playfield you will see a flat 2-wire connector with red/black wires.
Give that a good push together to see if it makes a difference. If it does, replace the connector.
Also, I would do a full switch test just to make sure you don't have a matrix issue.
Try to run through everything. Also, the optos in the MPF. They are a bit harder to get to, but with a friend you can lift the MPF up and get to the optos under the MPF to make sure they are working. Just block with something solid.
Watch your fingers working with the glass off.
faz