To close the loop on this --
TLDR; - It was a ribbon cable issue.
I bought a new replacement motor board. After installing the new board, I still had the same issue. Using the fwd and back test buttons on the new board, the motor did work as expected. This told me that the issue wasn't with the motor board, but instead upstream somewhere.
Back to the manual -- Looking at the manual, the clock is driven by solenoids 42 and 43. When 42 is on, the clock runs backwards. When 43 is on, the clock runs fwd. With both on or both off, the clock stops. Since my clock always runs in test mode, that led me to believe that there was a problem with solenoid 42.
On a whim, I went into solenoid test to see if I could test those 2 individually. Indeed, I could. When I turned on 43, the clock went forward. When I turned on 42, nothing happened. At this point I was certain that either 42 wasn't working, or I had a connector issue. I started with the easiest to diagnose, a connector issue. I reversed both ends of the ribbon cable from the CPU to the 8 Driver board. (double and triple checked that I had it installed correctly). Turned the game on and the clock now works, both in game as well as in TEST.
I had reseated the cable before without any luck. I suspect that there's a failure in the ribbon cable.
Just wanted to post the solution here in case someone else has a clock issue.