I tried to make a custom companion, I got all the scripts down as the walk-through on the CS wiki said, but whenever I talk to him I get the "I HAVE NO GREETING" issue, I tried attaching a Shivering Isles faction to him but that didn't seem to work. I put him down in the Imperial City Market District in the CS as his location, is it because originally I had him set up in Madness armor but then changed it?

If you have made your companion a custom, non-playable race he won't have any greetings until you give him greetings that are assigned for him.

You should then start a quest (the Q-button in the CS) and assign a greeting for him there. (see wiki instructions on how to start a quest)