When you say lubricated what do you mean? WD-40 is a HUGE no no in EM as it's not only flammable, but it gums up over time and creates nothing but problems.

If I'm reading this right you're saying that the ball count unit (the stepper in picture 3) isn't moving unless you manually cycle it? If so it might actually be the switch on the score motor that pulses the ballcount unit. On my 2 player gottlieb, it was a switch on stack 1A of the score motor (the wheel in picture 2) that was dirty and causing this behavior. Without the schematics though I'm not sure if it's the same switch.

Other things to check that could cause the score motor to run is the zero position switches on the score reels. It's a switch that should close when the score reel is set to 0. If all the 0 positions switches don't make good contact the machine will get caught in a boot loop as it doesn't think the reels are reset.

I want to say that the ballcount unit is where you should be focusing, but I only have experience with the gottlieb ems that used the AX resets, so I'm not familiar with how the reset bank plays in to the reset. I still say cleaning all the rivets and switches on the ballcount unit wouldn't hurt though.