Quoted from Tranquilize:

I've solved my auto plunger woes.
To the autoplunge crew: you're never going to get it to work 100%. It is a simple physics problem. The machine has very little leeway or space to nail the loop with the upper flipper in the way. On top of that, this machine needs more nudging than a child entering a haunted house, so the machine is always going to essentially change shape, and the table will never maintain a perfect level. If you have rubbers on the legs it will be worse because the legs cannot slide strait again after a nudge.
SOLUTION: hold the upper flipper up whenever balls launch. I get 90%+ balls around the loop with this simple learned adjustment. Hell, some even make it around when the flipper is down, but I don't expect them to. I also leave the flipper down when I want to gain control quickly to score a soul shard etc. To me, this is part of the game and is perfectly fine.
As for the manual plunger, it will change too. I find the light plunge skill shot the best bang for difficulty, so I never plunge for the loop. In my eyes, my game works wonderfully.
Think of all the ball'n beer time I have!