DigiKey does custom work like that for the connectors they sell. They do the wire-and-connector assemblies for me for the BoeBot Encoder. (I typically buy 500 at a time.) You will have to submit specs for a quote and sign a no-cancel/no-return (NCNR) agreement when you place your order, but they're very easy to work with.
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-Phil
Thanks, I'll try that.