Alrighty then. I decided to refresh my own memory and pulled both styles of drop target assemblies from inventory. In the pic below are the two styles side by side. The one on the left is the original 1981 design and on the right is the later 1983 revised design. This is how they look when removed from the playfield.
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As you can see in this next pic, the older design on the left has a smaller Molex connector than the one on the right. That is because as mentioned earlier the later design simply unplugs from the main wiring harness while switches and main coils were hard wired on the older style. Only the smaller individual coils utilized a Molex connector. This made the older style more of a PITA to remove because you have to unscrew all of the switches while the later style can be removed as a complete assembly (as shown in the picture).
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The next picture shows the fingers I described that bolt to the front of the drop targets that prevent the ball from getting hung-up between the drop targets when they are down. This was an improvement made to the 2nd design. The original 1981 EBD does not have these.
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From the bottom you can see another improvement that was made in 1983 with the addition of a bracket that allows the drop target height in the down position to be adjusted to make them more flush with the playfield. This again was added to prevent hang-ups and to compensate for variations in the targets and the stamped housings. Nice feature.
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Last but not least is the original question of this thread. Was there ever a rod in the hole with the arrow in this picture from the original post?
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The answer is YES there was a rod in that hole! It is the small diameter rod in the hole next to it. You have the rod in the wrong hole. The hole you have it in in your pic is a threaded hole meant for the spring bracket on the earlier style that is not used with the later revision. The rod is supposed to float around loosely in the larger hole (see pic below).
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That's why the hole has the marks in the plating like it does. All you need to do is to remove the rod you already have and move it to the larger hole to return it to the factory setup. As you can see by the pink arrows, the spring bracket was flipped around from the original style. This places the springs outward a little more giving them more tension on the retaining shelf in the up position.
So just take your rod and remove it from the hole it is currently in and move it to the correct hole (yellow arrow) and you should be good to go. Although I rarely have any problems with the original design these minor tweaks were made to the 2nd design as the result of complaints in the field. I estimate only around 2,000 pins made probably have the 2nd design. Part of the Limited Edition run and all of the Classic Edition final run. The other 10,000 or so have the original setup. That's why if you see one of the later versions of these for sale on eBay or somewhere it is worth snatching up these more rare assemblies because you can convert your original style to the later design.
As mentioned by others too, you can flip the spring bracket around on an older style and add a rod on your own too if you like. I don't because I never really had to but it is something that can be done if you feel you need it. But if you have target popping out of the assembly I would first determine if you have it assembled correctly.