Fixing some minor issues in your code makes the example work. Some of them were:

1. Linking d3js v5 instead of v3.
2. Making the svg position absolute on the same position as the map.
3. Defining a fixed radius for the centroids as there is no property Scale in your geojson.

Here is the cleaned up code showing your features on the map.

Fixing some minor issues in your code makes the example work. Some of them were:

1. Linking d3js v5 instead of v3.
2. Making the svg position absolute on the same position as the map.

Here is the cleaned up code showing your features on the map.