My GNU Shepherd configuration isn't as simple as it could be, but it's usable the way it is.
The scripts in /usr/local/etc/init.d are the same scripts as the corresponding runit run scripts.

The shepherd-init script is a workaround for a bug I encountered, where the GNU Shepherd refused to run as init
because a stale socket file from the previous boot wasn't deleted as expected.
I don't think the shepherd-init script is needed anymore.

Copy the shepherd.scm file to your GNU Shepherd's default config location, or specify where it is
like in my shepherd-init script when you run shepherd as init.
Modify the "init=" parameter of GRUB if you want to change the init system.