I own one of these and have done a complete mechanical rebuild and can offer a few observations-
It is the case that even in a completely shopped perfectly working stepper unit that occasionally the total reset coil will fire and the unit will fail to completely reset- its very occasional.
Three things can be adjusted that will effect this (at least)-
ALSO_ please note- during game play when the total reset coil fires and the end of stroke switch fires it activates a relay that should index the bonus up 1 position to 5K so you start at 5K for every ball- so its not supposed to go to a true zero for more then the length of time it takes the electronics to reset it from true zero to 5K. I believe that at the start of a new ball it may be zero but somehow cannot recall this (DOH. I have played this how many thousand times!!!).
(1)There is an end of travel switch that is closed when the bonus steppers reset to their zero position- make sure this switch is adjusted so that it does NOT close early-
This is the switch on the far right of your above pic that is contacted by the plastic end of the armature- (doubt this is your problem)
(2) The mechanism might be gunky or the total reset arm not fully engaging the mechanism (as you found)
(3) The wiper disc assembly has been over tightened and the brass contacts are slowing down the assembly or (same issue) the entire assembly has been over tightened and the movement of the brass gear is inhibited (could also be gunk).
(4)- bonus reason- Your stepper units have a brass screw with a square set washer (if its original- top right of your photo) that you can turn that will move the plastic armature and adjust its "at rest" position. If this is adjusted wrong the indexing of the end of the armature and the teeth on the gear will be wrong- it will advance and then sit either slightly pushing against the next step on the brass gear or there will be a gap (possibly large) between the end of the armature and the brass gear. This needs to be adjusted so that it cleanly indexes to the next position when you rapidly flip back on the coil assembly and most importantly so that as it comes back to rest- the end of the armature that contacts the advance teeth on the brass gear are nicely resting right on the gear- not with a big gap or holding it against spring tension.
(5) bonus reason #2-
This is one of the most complicated games ever made in the EM world- There are many many failure points. The bonus units your working on are the heart of the game and everything needs to be perfect- then it will play great.
With regard to the flippers-
YES_ Williams flippers when held open and then subsequently hit with a ball will ever so slightly come back contacting the EOS switch and activating the flip coil causing the ball to "bounce" off the flipper as it closes the switch- this is a fact of life for these ERA assemblies and there is nothing you can do to "fix" it because its not broken.
You CAN replace the mechanism with a different more modern design that "fixes" this
I suggest you leave it alone- thats actually not a very commonly used type of trap in this game and you will build an appreciation for these flippers if you play it a lot-
With regard to the spinner units-
A properly adjusted spinner unit on this game is capable of about 90 rotations with a seriously good hit-
Three things to ensure this-
The switch under the play field should be adjusted so that as the spinner comes through horizontal the contact BARELY touches- If your making firm contact your taking energy out of the spinner mechanically at every revolution.
The bend in the long contact is NORMAL- The arm going from there to the spinner should be straight and VERY LOOSE in its hole in the switch under the play field- it should DROP out without touching it if you remove the spinner assembly from the top-
The spinner itself should rotate freely and you need to be sure all the wire is perfectly aligned and the frame is not putting pressure on anything that moves
The arm from the spinner to the under play field switch should NEVER contact anything (like the wood of the play field)
Hope this helps-