If turns out the saucer switch and the pre-saucer switch are okay you might check the trough switches especially the last position where the ball is served to the shooter from. Saw someone in here have similar saucer troubles and that switch was causing them though it didn't sound like the exact same problem.
<<I can get the saucer to eject by manually holding down the switch right before the saucer for a second or so.>>
Does that work 100% reliably? When I had a Xenon I thought that switch made the saucer ball eject instantly, not after a second or two so perhaps that switch is the issue as mentioned, and is just dirty and/or undergapped.