Help With Atlas FM Erie Built (3-Rail)

I think they are part of coupler.  

Those cylinders look like the plunger for an electrocoupler.  How they ended up outside the couplers is a total mystery!

The easiest way to extend that cable if you don't have a crimp tool for the JST connectors is just splice an extension in the middle of the cable.

Yup, you guys are right on the money; each unit had a coupler that was bad to the point where they broke from where they get attached to the trucks via the plastic pivots. And when I looked inside the couplers that didn't break open, I saw the same little cylinders inside. Thank you very much, I just wanted to make sure it wasn't part of the drivetrain or the electronics.

As for the plugs, splicing sounds like a good idea, but I'd rather avoid doing that if I can. I'm assuming the plugs can be found on the Molex website, so I'm gonna try looking there, and if I can find them, I'll just make my own extensions.