OK, so I finally found the problem. One of the plugs had a wire connection that was not gripping the pin well enough so there was faulty connection that would come and go. Hence, the reason why I would get continuity when I had the train upside down but then it wouldn't run on the track indicating no continuity. So I puled the wires out of the plug and crimped the connectors and put them back in and now it runs with all four sections.
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