Ok, I have tested this further and I have found that if I trigger the right crane limit (switch 61) and the right flipper switch (switch 64) at the same time, the shooter lane (switch 16) is also triggered. If this happens outside of switch test mode it causes the ball launch coil to fire as it thinks there is a ball in the shooter lane. When tested on their own, all of these switches test fine. This may or may not be a separate issue.
In game mode with the glass off, I have found that the flippers stop working immediately when the crane right limit (switch 61) and the middle scoop left (switch 57) are closed at the same time. BUT NOT IN ALL MODES??? For example, in multiball or ball save modes it seems to operate fine until the end of the mode, and then the crane right limit and middle scoop left immediately stop the ball.
This says to me that the issue is telling the machine the ball has drained down the centre when it hasn't. Further evidence that points to this is that there is NO tilt shown on the display, just end of ball immediately as the middle scoop coil fires. I have used my DMM to run a basic test on the trough diodes, and they appear to be fine.
So I put the machine in switch test again, and when I simultaneously trigger the crane right limit (switch 61), crane limit left (switch 60) and trough #5 (switch 13) then trough #4 (switch 12) triggers also.
I have tested the switch diodes for the middle scoop left, right crane limit and the shooter lane, and they are fine.
I have never dealt with a switch matrix issue before, and I have now spent several hours reading up on the switch matrix.
I do try and fix any issues without doing all I can independently first, but I'm struggling here. Could anybody lend me some wisdom of where to go now???