I feel your pain. But in reading your symptoms, I immediately start going through images in my head of relays and switches.
My chime for 100 was locked, and it was a switch on the left edge of the playfield. Makes sense, since the chime can't go on, unless the circuit is completed.
On the score reels, I tell ya, they have to be set right, or cleaned, or they simply don't work.
I'll tell you another situation I just had. I got minty fresh drop-targets All excited I powered the game up, after install, and my drop targets would score as they dropped, but would not reset. My heart sank. But, I turned it off, and using my meter, I made sure each switch was making contact. Amazingly, some were not, but even more crazy, two looked like they totally made contact, yet no matter what, it wouldn't show as a short on the meter. I finally bent the end of the switch out a bit flatter to contact the other switch on a different spot, and voila, both started working, using that technique, and the bank reset!
On the score reels, I learned a lot about testing. A great way to see if things are working, is to simply tap the score relay by hand. So in the back, middle area on the left, you will find the 10, 100, and 1000 relays. With the game on, tap them. Your reels should fire. If not, power off, take the relay OUT, and clean and gap both sides of the switches. You can also check on your resets, to see if the score reels are getting the correct connection by using the score relays to get the reels off zero, then pressing the reset relays to see if your score reels start to reset to zero. At zero, they will stop, and the reset relay will do nothing. I noticed that there are two reset relays, that affect 2 score reels each. Left does the 1st and 3rd....right does the 2nd and 4th.
I learned on the reels that the switches must open and close correctly.
Zero = Open, Open, Open
1-8 = Closed, Closed, Open
9 = Closed, Closed, Closed.
I had all mine set correctly, and then I decided to tighten the switch stacks. MANY were loose and I was quite pleased with myself for finding these loose, sloppy switch-stacks. My elation faded quickly, as I realized the tightening of the switch-stacks, destroyed most of the switch gaps on the reels! Sooooo...I took out every single reel, painstakingly adjusted every one of them (that needed it), and now I know they are ALL adjusted and tight.
I learned that the steppers are sensitive to old grease. They either don't increment correctly, or more likely, when the reset coil fires, it doesn't reset to zero position. Cleaning was fairly easy. I used alcohol and then lubed them, and life was good.
I turned it on last night, and my 100 chime is locked on. I turned it off and watched a movie Lol! But, going back to it, I will look for a switch I was a bit too overexuberant in setting, and find the one that is touching, and closing that circuit. I like it to play "hot," so I gap my switches close, especially on the slingshots.
My final hurdle, is the chime box. I got a rebuild kit but I screwed it all up, and it sounds like crap. I learned from that, especially that you don't tighten it down really hard, (crushing the brass inside). So, I have a new kit coming, and this time, I will be much more sensitive to how tight I screw them down.
It can be VERY frustrating, and the schematics are slowly becoming more clear, but they still are daunting. As my second EM, and probably third EM repair, this machine was amazingly hard for me to fix. But as your immersed in the frustration, and reading, and posting, and measuring, and eye-balling....you realize after it's fixed, how much you learned, because it WAS a hard to fix issue(s). My purchase of Captain Fantastic was brought on my my realization that EMs are not slow and klunky like I thought, and the fact that I learned to repair a couple hard issues on my Klondike, gave me the confidence to buy another. I knew this one had issues, but they turned out to be much tougher than I thought.