You'll first need to determine what switches are sending power to the score motor. All the score reel switches should be in the same position when they are set to zero. Check the following switches to make sure they are open:

Coin chute switches
Drop target switches
Top hole switch
Outhole switch

The flipper circuit has only a few switches. Check the flipper button switch and the EOS switch to make sure they are clean and adjusted properly.

For the drop target scoring, you can manually operate the drop target relay to see if it will send power to the score reels.

Also, check all the Jones plugs on the machine to see if they are clean and fully seated...