A couple of things:

Perform switch matrix input test to isolate if switch problems for the sounds could be caused by playfield diode issues or on the driver board itself.
You need to test the switch inputs at the PIA itself. The inputs are on PIA II (IC11), pins 2 through 9. To test input #1, ground pin 9 of 2J3 and then using your test LED or Logic Probe, look for a pulse at pin 2 of IC10. Then move the ground to pin 8 of 2J3 and check for a pulse at pin 3 on IC10. Continue moving the ground down a pin and checking the next PIA pin (PIA pin 4 to connector pin 7, etc).

Remove and replace Scanbe sockets if you have them.
http://pinball.flippers.info/system6repairpart4.asp#scanbe