You mentioned that the ball got stuck on the switch at the right end of the return trough. That should never happen. If you want, you can try adjusting this switch to put it back to factory spec while you have the card holder (AKA apron) off of the game. It's not that difficult to adjust, but it might take a bit of futzing to get it right.
Turn the game off and put the PF down into the normal playing position. Set the ball on the return trough, to the right of the peak in the trough, and to the left of where the switch wireform protrudes up into the trough. Let the ball go. Gravity alone should start the ball rolling to the right, over the switch wireform, and into the shooter lane. If the ball doesn't roll out of the trough from gravity alone, the long switch blade of the trough switch is pushing against the wireform too much. Adjust the pressure of the long switch blade so it isn't pushing quite so firmly. When you have the blade adjusted to a low enough tension, the above test will work and the ball will be able to roll over the wireform from a dead stop just by gravity.
On the other hand, you don't want to make that long blade tension TOO low, because then the vibration of the game play might cause the switch to close when it shouldn't. So you need to have some tension on the blade, and a decent switch gap, but also have the switch so that it makes a good solid closure when the ball rolls over the wireform, and also so that the ball can't get "caught" on the wireform. Like I said, you may need to futz around with it a bit, but it should not be that difficult to get it dialed in properly.
That additional red wire was just some hack someone did to try to fix some problem, or make some mod. Later, someone else (thankfully) removed the hack. In any event, you don't need to be concerned about the red wire as long as it doesn't touch anything. You probably should clip it off.
- TimMe