Hey, philinchio, welcome! I hope we can help.

I don't know the game at all, but from your description, I'm wondering if anything scores/chimes? What does, if so?

If some game features aren't scoring/chiming and some are, I would inspect whatever relays controls the scoring for the non-working features. For example, on 2001, when a drop target is struck, the 50-point relay pulls in, which spins the score motor, and five pulses are sent to the 10s chime and the 10s reel on the scoreboard. If the non-working game features all have some score in common, you might be able to isolate the problem to that relay -- or rule it out.

One thing further: do you have a schematic? That would be very helpful.

I think this is what I was trying to say upthread, and stashyboy was as well. The features you named as working correctly (scoring and chiming) are all 500-point features. The others (10s, 100s, and 1000s point scorers) are not working, correct? Inspect those relays. Your schematics will identify which ones they are, if they're not properly labeled themselves. With the playfield up, trigger one of them (a drop target for example) but observe 100 and/or 1000 point relay -- does it pull in? Are all of its switches changing over correctly?

And also, like CactusJack said, check your jones plugs -- all of them! And even if they look clean and they're plugged in correctly, give them a good scrub with a wire brush and reseat them. You might fix some problems that you don't even know about yet.

You're not going to mess anything up. Scrub scrub scrub!