Thanks for the input everyone! It’s actually the “I” relay that is in question. So a local guy actually had a spare gear in a relay from a scrapped machine. Stupid me takes it apart, and not thinking clearly, I didn’t take any pictures of the black cogs or which way they went back on. Duh!
Now the bonus doesn’t go through the entire sequence. Before the bonus would go through the entire sequence from 1 to 5 thousand, and not score any bonus that was lit. Now it scores what seems to be only the three thousand only if it’s lit, and kicks out the next ball.