I've done ee site update sites.domain.com --letsencrypt to enable SSL but obviously this doesn't cover the custom domains. I've tried using your shell script with the proper domains to get it going but it's just not working. I've tried --letsencrypt=off in case too but no dice. Any extra pointers?
Do I need to use the WordPress MU Domain Mapping plugin if the WP I'm running is 4.7.2?