I have https://wordpress.org/plugins/wordpress-mu-domain-mapping/ running on my build and it was working great, but I had to switch my primary site - point / to another site ID - and now my custom domain is just directing to the main site.
I'm not sure what I can include here for reference but if anything has any idea and needs more information, just let me know and I'll get it for you.
My mistake: I installed an SSL certificate that was directing all traffic to the specific domain.