I don't know what the hell happened with my last post but here it is again. I was having the exact same problems as you. The damn game wouldn't quit feeding balls into the left VUK and feeding the flipper for eternity. All the tests checked out fine with the balls in all of the VUKs as well as the trough. Here is the idiots guide to troubleshooting this as it worked for this idiot (yours truly)

1 Take out all of the pinballs (6)
2 Put the menu to switch edges
3 Hit the playfield firmly with your hand a few times, don't be shy

In my case, the l.lock #4 was the errant switch. I used my phone and all of the LED transmitters were glowing just fine so I jiggled the wires on the recievers (black side) and was able to reproduce the error. Good luck! I haven't played STTNG for a year because of this. It is good to have it back.