got time for lots of highest possible resolution pictures of everything (playfield, backglass, cabinet front/sides, internals)?
monaco has some terminology differences to the bally games, but what you care about for payout is the area on the schem around D14. You need the scan index coil to power and stay powered for the duration of the payout.
the way it works is:
1] scan disc wipers are spinning around and causing the row relays to power as balls are detected in holes (chatter in BCP post above)
2] if 3+ adjacent row relays power at the same time and the game has not previously paid to the score level for that detected win, the scan index coil is powered and stops the scan wipers on the rivets
3] the replay index coil is powered and pulses on the replay cams step up the replay register (add credits) and step up either the card replay control unit or the super card replay control unit, depending on the win and whether those wins score separately (separate score feature enabled)
4] when the stepping replay control unit steps far enough - determined by the position of the score S.U. unit - the circuit to the scan index coil is broken, which also breaks the adding credits circuit.
one handy diagnostic is to set up a win and if it pays anything, manually reset the appropriate replay control unit. It should win detect and pay again. If you are getting short pays and suspect flaky connections on the replay control unit wiper->rivet interface, doing that can give you different pays. You can also wiggle the wipers and see if pay continues.
as BCP said, any cruddy connection on stepper units or the scan discs will bite you, so clean all the rivets.
assuming at least some of the stepper units are snowshoe style - the peg wipers with springs - check and see of the wipers have grooved or cut through the rivets. Getting a decent connection between the wiper pegs and the sleeves is a hassle. Sometimes people soldered flexible braided wire - kinda like solder wick - between the tops of the appropriate pegs so they didn't rely on the sleeve connection. I've had the best luck removing the pegs and cleaning the edges and sleeved hole with a wire wheel.
finally, note there's different paths thru the row relay switches depending on which holes the balls are in. If you find some numbers on a line pay right but others don't, could be a poor switch on one of the row relays or the wiper->rivet connections on the scan disc.