Speaking from personal experience, adding software is non-trivial, because the CD itself is a Yum/DNF repository and you have to regenerate the metadata. I believe the tool you want for handling that is called createrepo
[1], but I'm not 100% certain about that (it's been a couple of years since I had to do this myself, and I wasn't smart enough at the time to document it...).
Removing stuff is easy as long as the install doesn't try to use it, you just remove the packages.
As far as customizing the install, I would suggest checking out Kickstart [2], as that is how most of the scripting and automation is done, it's probably also the easiest way to get a custom install.
[1] http://createrepo.baseurl.org/
[2] http://pykickstart.readthedocs.io/en/latest/