I think I am getting close!
Left sling shot registers as left sling and missle
trough 2 registers as trough 2 and trough 3
trough 3 registers as trough 2 and trough 3
and the missle registers as left sling shot and missle
All the other switches seem good.
Yes you are getting close, but it seems that the origonal problem is still there.
Make sure that you are in switch test mode in the diagnostics menu
Test the cpu board by removing CN8 and CN10 and using a jumper wire to go through all of the combinations on the switch matrix. If these all register correctly, then the problem is not on the CPU board. (see page 50 in the manual)
Remove all of the balls from the trough (there is a trough clear function in diagnostics)
Reconnect the CN8 and CN10 connectors on the CPU board
Now, go through all of the switches on the matrix using the switch diagnostics, paying close attention to the switches on rows 2 and 3 (where the issues are)
Carefully inspect the diodes and wires on the switches and make sure that they are not shorted to anything.
You may need to take the gun handle off of the machine to look at the wires inside the gun that go to the smart missle switch to see if the problem is in there.
Good Luck