I was having the same issue with the same score reel on another Williams 4 player game and I was able to correct it quickly. None of the 10 place value scores would trigger on any of the 1,2,3 or 4 player score reels, so I knew it wasn't just the 10 place value reels.
After I found the schematic online, I discovered that it was a foul contact in a relay. The backbox on all of the Williams EM games that I have each have a different relay for each place value score reel (1, 10, 100, 1000, etc.) The 9 digit will rollover to 0 and trigger the next higher place value relay to go up, so chances are, the 100 place value score reel is doing it's job, but the 1000 place value relay isn't detecting the signal from it.
If you look in the back box, you should be able to identify a bank of relays that are labeled for each place value. Inspect the solder connections on the wire to the 1000 point place value relay. If they are ok, clean the contact on the magnet of the relay with some emry cloth or something. You can even start by manually tripping the relay with your finger a few times where the plastic bracket holds the leaf contacts. Do it a few times with the machine off and see if that frees up any corrosion in the relay, then turn it on and test it out.