I downloaded a shape file from the U.S. Census and passed it through http://mapshaper.org/, which gave me a working topojson file to use in D3.
However, I realized the topojson file had all the features labels stripped. So there is no way identify features to link to CSV data.
I installed topojson, but topojson version 2 does not have the same commands as the version one to convert shape files to topojson and retain the features. Previously, topojson -o output.json input.shp This is the current topojson github reference https://github.com/topojson/topojson.
So my question is what is the best way to convert shapefiles to topojson and retain the features attributes.
I'll answer in relation to the mapshaper method you've used.
The problem as I understand it is that you are losing attributes/properties contained within the shapefile when converting to topojson, such as feature id or name which breaks links to data in other files.
When using mapshaper, you need to copy the .dbf, .prj and the .shp files that come with the shapefile into mapshaper. The .dbf contains all the attributes/properties of the features. This will ensure the topojson has the properties that the shapefile does.
If there are too many attributes per feature and you only want one or two of them, then you might need to use another piece of software for that action (or another to both remove attributes/properties and export to topojson).