Yes, the left bonus unit on most machines are out of alignment because people rest the bake light square on the cabinet sometimes. That is a quick hand adjustment to get the bake light squared again. It can happen on any of the units, but that one is the most common because of its location.

As far as your left unit, it sounds like one of the EOS switches is not activating the end of ball/reset sequence.

When the bonus goes to 0, it hits a switch to reset the bonus to 5K and closes the R Bonus reset circuit. Look at section 15 on your schematics. Check to make sure that switch is working properly. Look for R. Bonus Unit Zero Bk

Since the left is working you could compare them visually.