Logged in to update site, noticed most plugins are missing?  Not sure if there is a reason for that...?  No iThemes Security, etc.

And none of the site settings - timezone, city, day of the week...it's all still default.

I'm not sure what would have happened. I know we had the login page, so I assumed everything was there. 
With multisites, are the site settings done per-site or done on the main network settings and carried through? Was the main site settings page completed or none?

You have to set up each site individually, all the settings pages (read, write, permalinks, etc.)