I'd go through the stepper for the right bonus. Make sure it steps freely, sand the contacts, etc.

Also, check the zero switch on the right bonus unit. Make sure it's sitting properly only when the unit is fully reset. I don't recall if it's open at that point or closed but either way, it should be in that state only at full reset. Once it moves up even one spot, that switch should change state. If not, it might not think there were any points and not fire the kicker.

As long as the contacts are shiny you're good.

Compare the right bonus unit with the left. Is the left 5000 always lit up? How does the left's zero position switch work compared to the right?

The fact that you said "doesn't kick out when bonus is zero" may be part of the problem. The bonus should NEVER be zero, at the beginning of a ball or when it is collected it should always be at 5000 to start. The problem is definitely in the bonus counter, compare the switch open/close settings at each step to the left side to make sure they're the same.

Both of them hang on the bottom of the playfield, one for left and one for right.

The bonus always starts at 5000.

That behavior generally means the unit is gummed up with old grease and dirt. The ideal solution is to disassemble the unit, clean it and re-assemble. This is tricky because everything must go back in exactly the right place and in the right relationship with each other. You may be able to get by with something less.

First, reset the unit all the way, by hand if necessary. On the side with the circuit disc, pick one of the wiper fingers and mark it with a Sharpie. Put a matching mark on the circuit board. Then you can remove the nut and pull the wiper unit off the shaft. Make sure the ratchet wheel does not turn while removing the nut.

Now take some 600 grit sandpaper and sand the rivets until clean and shiny. Don't sand off your alignment mark! Wipe the board down with isopropyl alcohol and then spread a VERY thin coat of Teflon Superlube over the rivets. Clean up the contacts on the bottom of the wipers with a flexstone or the same sandpaper. Don't bend the fingers while doing this.

Reassemble the unit, matching the marks you made earlier. Now, step the unit up a few notches and then reset it. It should spin back all the way to zero. If not, you have two choices. Disassemble it all the way and clean the main shaft or, the inadvisable way, tighten the clock spring one turn. That should be a last resort as you want those units to operate with as little spring tension as possible. Tightening it may make it hard for the unit to step up - you'd just have to see.

We probably need to start at the top and go systematically. When you drop the ball in the hole at the top on ball 1 of a new game, the bonus should advance on the left side and the left side red arrow should be lit up. How much bonus do you get? Catch the ball when it ejects from the top hole. Now drop the ball in the drain. That bonus should count down and be added to the score. Does it? What is the state of the bonus lights at the start of Ball 2?

Ball 2 now - the red arrow on the playfield should have switched sides. Did it? Put the ball in the top hole. Did you get the same amount of bonus on the right side? Drain the ball. Did it count down and score? What is the state of the bonus lights at the start of Ball 3?

Repeat just those steps for the rest of the balls. The arrow should alternate sides and you should get bonus of the same amount on all balls as long as you catch and drain it before it hits anything else. The state of the bonus lights as each new ball starts should be the same. Let us know what happens with that.

Start a new game. Do the same thing but this time, after catching the ball, knock down the 2 upper drop targets by hand. The 1 Star light should come on at the bottom of the playfield. Does it? Drain the ball and check that bonus scoring is now double. Is it? Repeat for the rest of the balls. Try the lower drop target pair at least once. Bonus should double and the 1 Star light come on when either the upper or lower pair of drops is knocked down. Does it?

Start another game. Drop the ball in the top hole and catch it when ejected. Spin both spinners by hand to max bonus. The spinner lights should come on and spinner values go up. Does that happen? Now drain the ball. The left bonus should count down and be scored. The right bonus should just go away. Does that happen?

Light sockets are certainly a probable issue. You'll likely need to clean them at best, replace some at worst.

It's good that your alternating logic is working and most of the bonus functionality seems like it's trying to work. I think you are definitely looking at some sluggish and dirty units. I'd start by cleaning both bonus contact disks and the wiper fingers and giving them a light coat of the Teflon Super Lube. Do the same with the Ball Count unit. Make sure it looks like all the wiper fingers on all 3 units are making good contact with the rivets and the units reset smoothly when asked.

On each contact board, check to make sure the wipers are sitting smack on the middle of the rivet when reset. There are three screws on the contact board that, when loosened, allow slight rotation of the board. If needed, do that so that the contacts are as best centered as you can make them. Look at the general alignment of the contact board. It will likely be more or less square with the frame of the unit. Take note if one looks to be rotated a lot in either direction but don't fiddle with it yet. Just get them centered on the rivets. Then let's see where we are. It's possible you might be a rivet off on the one, but don't mess with that until they are cleaned and moving freely. Start there...

Ha! That's the same "fix" that was on mine when I got it.

The hole at the top of the playfield is supposed to advance the bonus and it is adjustable with a plug for two or three advances. So, if you're at 5000 on the bonus that's lit at the top and you land in the hole, it will advance the bonus to either 15000 or 20000.

The hole itself scores 5000. However, it will advance the bonus depending upon which side is lit up by the hole. Just to make sure I understand you correctly, it's only advancing the bonus on one side, correct? It shouldn't be advancing both sides at the same time.

That's correct, and it's set on the conservative setting. If it was set on liberal it would go up to 20000.

I had this exact issue on mine. Try taking one wind off the clock spring on each of the units. You will see where the spring hooks onto a post. Lift it off and unwind one rotation then hook it back on. Make sure the unit still resets backwards as it should then try again.

Mine had such tension it was passing multiple ratchet teeth at one time.

When the bonus units were gunked up before you cleaned the circuit boards, someone decided the cure was to ratchet up the spring to force it to count down. Once you cleaned it up and it stepped easier, there was too much spring pressure so it counted down erroneously. Good lesson on how not to fix machines.