Hi Rob,
I have a couple of suggestions. If you are losing the left flippers, there are only about 3 main thing which could cause this.
I suspect the flipper problem may be related to the dodgy Q relay. For viewers which have just tuned in, I had a look at this for Rob a few months ago, and found this relay has some residual magentism and would occasionally stick on even when the power was removed. We were eventually able to adjust it and get the game working but it was very difficult to adjust the switches (much more than it should be) to work around the relay sticking. I would definitely suggest trying to replace this if other collectors have a spare.
Looking at the schematics, the ball count unit could also be a problem. The schematic shows there are actually 7 positions on the stepper. The is a "Ball 0" switch on the stepper(somewhere on the unit), the 1-5 ball positions and a position 6 (game over). Does the ball in play lights work correctly after adjusting the stepper? It might be worth re-checking the stepper adjustment and switch on this unit.
The flipper contacts were almost non existant on the flipper switches so might also be worth checking/replacing these. There wasn't much left to file.
Hang in there Rob, you are close to fixing the problems which have been on your game for a long time! Once all the problems are ironed out it should be reliable for a long time.