Did you see it work? There appears to be some rewiring on the main motor (all of the white wires).
If you saw it work, I would start be re-seating all of the 'jones plugs'. Clean them up first if they show signs of dirt/grease. Be careful - Chicago Coin parts are quite cheap and fragile. I've broken my share of tabs on the female end of these by trying to slightly bend them back into location.