The built in test modes are your friend.
Run the solenoid test mode and note down any coils not activating or activating at the wrong time. Only then can we build a map of what's logically going wrong.
When you have switch issues, you need to make sure you're starting from a blank canvas with switch test mode reporting "0" closed switches. As above, if a switch is being reported as closed but it isn't, if that switch has a capacitor then temporarily clip one of the capacitor leads.
Once you get "0" closed switches, begin activating them starting from the highest number switch working your way down as per the switch numbers listed in the manual. It's important you do it in highest to lowest order on these old Ballys/Sterns because switch test mode only reports the lowest number switch it finds as closed even when there are many closed switches.
If a switch reports the wrong number and you have drop targets down, raise all the drop targets, and drop one target at a time to see which drop target is affecting the wrong number switch being reported. That drop target may have a shorted or backwards soldered diode on it.