The following modifications are major changes to migrate to 3d.
1. networks/Mesh_3D.*
2. routers/ThreeD_router.*
3. routers/routing_algorithms_3d.*

There is an example config file inside examples/pras/

To run hotspot traffic (treating center node as hotspot), 

./booksim examples/pras/3dmesh traffic=hotspot hotspot_percent=0.08