You just use the ArcTool arcpy.management.AddSpatialIndex(). The help explains it will rebuild an existing index. Since the indexing is simpler you don't need to specify the spatial grid sizes. I have done this after loading data into a large featureclass and it makes a huge difference to drawing speed and processing.
If processes appear to hang it is always worthwhile to interrupt the process, rebuild the indexes (including attribute indexes) and restart the process. Never be happy with any tool that takes longer than a cup of coffee. Find a better way.
Note that you need to ensure that your features are small and contiguous relative to the full extent. If you have a large 'Mozilla' feature such as an enclosing coastline or large area punctuated with 'holes' representing forest you will defeat the spatial indexing. This is what the DICE tool is for, to split up unreasonably large polygons.
The same applies to polylines. A single line representing a national highway included with short local roads will make all processes that use an index be very slow. Also do not be tempted to dissolve by a single attribute to 'normalize' the attribute table where one zone is represented by thousands of multi-part polygons.
Running processing across a network is likely to be very slow. Process locally, which means: extract, process, replace.