Ok I traced all the wires by hand and using the schematics. All the
wires line up for connector J3 on the transformer board going to the
all the other boards. Except for one exception.

I have the transformer wire from a2j3-13 going to Solenoid Driver
board a3j3-5. The plug connector schematic says its supposed to go
from a2j3-13 to SOL. BUSS

I have no wire at a2j3-9. The plug connector schematic says its
supposed to go to a3j3-5, a8j1-9.

Thoughts? Would this cause my issue possibly?