This is an informational post for future confused pinheads. It applies specifically to my Williams Stardust (1971), but I imagine it should hold true on most Williams and Bally EMs, also.
If you take both your Coin Unit and Count Ball Unit apart at the same time to clean them, then find they don't quite touch all the traces they're supposed to on the bakelite after you put them back together, check the number of teeth on the main clock gears. At the reset position, the Coin Unit gear has four teeth (for 1-4 players), then a smooth toothless area. The Count Ball Unit has six teeth (for 1-5 balls and a game over position), then the toothless section.
This may seem painfully obvious, but it was giving me fits last night. I had mixed up the gears, but the Coin Unit had enough traces that it didn't seem wrong for it to count six positons. When I got to the Ball Count, and found it was two positions short, I realized my mistake. A quick gear swap between the two steppers and all was right with the world.
It's also worth noting that the Ball Count stepper does have a blank section of bakelite it passes over, so it's not misaligned just because the wiper on the spider doesn't touch anything in one position. It doesn't need to know when it's on ball two, beyond lighting it up on the backglass, so the bakelite is bare there.
Again, maybe exceedingly obvious, but I thought it might be worth clarifying for any other poor fellow who comes upon the same problem down the road.
The moral of the story is to always inspect the alignment and action of your steppers, even if you think you got it all back together right.