I had similar issues with my Stargate in multiball that ended up coming from the optics being intermittent . Which took me awhile to figure out as they would read about 80 percent of the time. After reheating them all it fixed that problem. Also doing the ground really did help take care of the rest of my woes with gameplay. Honestly though it is hard to say for certain if it was the ground mode or other connection reheats that helped more. My machine was in very poor health when i got it and with my experience of cold connections in the past, just went ahead and reheated all weak points in the game.
Will be interested to see hear if that new MPU board helps.