You can build the time delay yourself. The cap, diode, and resistor are readily available anywhere and you should be able to find an old jones plug on Ebay. Here's a diagram of how it should plug into the machine. I don't believe this part will affect scoring on your spinners though - it's just a time delay to prevent other "events" from occurring when the spinners are active. The scoring problem probably stems from the AS relay being improperly adjusted. They can be difficult to dial in.
I suspect the bonus score issue would be the switch I have highlighted on the "Q" relay. That leg of the bonus scoring circuit should fire regardless of which ball you are on. The 4B switch is working since the red hole scores bonus properly. And the other legs of the bonus scoring circuit seem to be working since your end-of-ball bonus increments properly on ball 2 and 3.
The extra decrement could very well be switch adjustment problem on the ball animation unit. The wireform switch actuator should be adjusted as low as possible in the rail. If it is high, it will bounce violently when balls are pushed off of it which could cause the switch to make. Actuate it with your finger to see if you still get the extra decrement.