OK, lets start from the top... As the landing count is inconsistent, there is probably lost sensor counts due to a failing reed switch or from motor or grounding/shielding RF noise masking the sensor counts. We need to identify where the problem originates. Since the PCB was tested prior to shipment, I would suggest that we initially proceed on the assumtion that the controller hardware is working correctly.
When reassembling the ASC1, did you make sure that the ground connection from the transformer base was firmly seated to the AC junction/fuse assembly?
Did the actuator and controller work properly together in the past or is this a new install or new components introduced to the system?
Is the dish position count accurate if the controller is out at the dish vs through the wiring into the home?
Does the dish drive long and stop past the target satellite actual position or does the dish stop short before reaching the satellite actual position?
Is the dish connected to a grounded rod?
Is the dish bonded to the home utility ground rod?
How is the actuator power (M1 and M2) wires run to the dish? In a bundle with sensor or a separate wire?
How is the actuator sensor wiring run to the dish? In a bundle with the motor power or a separate wire bundle?
Where is the sensor bundle shield drain wire connected? Controller, actuator, both ends?