Update:
OK, I discovered what the problem is but I have not found out how to get around it. The issue is that some of the files are tagged my mac as unsafe (cause they are not from the App store or approved developers) and thus are blocked by permissions. I have granted access to each one whilst the installation is running but unfortunately this provides an error for the set_up. Running it again pops up the same permission issues and I cannot, for the life of me, figure out how to ttell Apple that it is OK to run these