I had what sounds like a similar issue with bonus countdown as you have. I started his thread and the guys had me fixed in no time......also make sure the switch on the bonus unit is closed...and closed tightly...it should open when the 15 position is reached by an arm/lever on the gear wheel. If dirty or not making good contact the vibration of the stepper could cause similar stop and go issues countdown issues.
https://pinside.com/pinball/forum/topic/tech-em-help-target-alpha