Quoted from Tony3Quarters:when the ball drains and all the reset happens, the lights and the bonus stepper counts down with no problem, but it does not ADD the 1000 points per light as it turns off the bonus lights.
Inspect and diagnose this circuit with Alligator clip jumper wires
http://www.planetimming.com/Pinball/troubleshooting/EM%20Troubleshooting.pdf
http://www.pinrepair.com/em/index3.htm#features
Example of a pinsider actually doing this https://pinside.com/pinball/forum/topic/red-baron-tech-question#post-5858156