Joe, timely post as I am trying trying to figure out who makes those connectors. It would help if you posted a pic of the exact connector.
Lionel uses are least three type of those small connectors. Some made by Molex, some by Leoco, and some by brand ???. The ones used in one of my engines have .1" (2.54mm) pin pitch and have a camphor on two corners. MTH uses these same connectors so hopefully G can help us both out. Most of the Leoco's have 2mm pin pitch and are used to connect wires to boards. I think the ones similar to Leocos but with a 2.54 mm pitch are Molex.
Connector X is shown as H or L in this image. Is this the same one you are looking for?