Well...after playing the game for a bit I noticed that when the red and yellow are paired on 100 and the center target is hit, no points are added. I manually tried all combinations and 100 is the only one that does not work. The subway doors open, but no points are added. The score reels will count up from 90 to 100 and if the center target is hit at 200 or 300, it scores properly. So I am guessing the 100's relay is OK.
Because the score motor does not move when the yellow or red bumpers are hit, I have eliminated it as an issue. It points to the 0-9 stepper or where the current flows to when the 100 is paired. I have cleaned and checked the stepper pins for alignment. Help appreciated!