Why not use the standard connectors used by Lionel for all their TMCC stuff? They use JST-EH (2.5mm) and JST-PH (2.0mm) for most TMCC stuff, once in a while you'll find the smaller JST-ZH (1.5mm) connectors. Legacy mostly uses JST-ZH and Molex PicoBlade (1.25mm), though there is still some JST-PH connectors in some models.
You can get all of this stuff from Digikey, and I use the Engineer PA-09 or IWS-2820M AWG 28-20 crimp tool, both available on Amazon.