You have installed your beloved ports during stage two. Some ports require a little bit of configuration. This is what stage three, the post-configuration is for. I could have integrated this post-configuration at the end of the stage_2.sh script. However, I think there is a conceptual difference between installing a port and modifying its out-of-the-box configuration that warrants a separate stage.
I have chosen to implement stage three as a Makefile because this allows easy selection of what you want to configure simply by running:
As with stage_2.sh make sure you have stage_3.mk available after booting the new system, either by putting it on a shared partition or copying it somewhere on the new system.