Nothing looks out of the ordinary with switches.
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Quoted from Mr_Positive:3. Do you have a multimeter and know how to test diodes with it?
ANSWER: Yes and Yes.
Ok, so check the diodes on all three trough switches, outhole switch and both saucer switches.
When you go to solenoid test mode, do they activate in correct order as per the manual?
Switch matrix issues manifest themselves when more than one switch is held closed (i.e. like a stuck switch/shorted capacitor on a switch, a fallen drop target or balls sitting in troughs/saucers - likely your case). Unfortunately the Bally switch test doesn't report all switches it senses as closed, only reports the lowest closed numbered switch.
So in switch test mode and with all three balls sitting in the trough you should be seeing switch 28 reported as closed, if you now activate all switches from 25 downwards one at a time, do any switches report the wrong number?
Report your findings to number 6. above.