The custom .css theme got picked up, but I had to enable the custom CSS option before that happened. Workspaces, plugins, hotkeys, etc. all have to be set manually.
I have a folder on my hard drive that automatically gets synced using Druva InSync. I copied my entire vault folder there (including the .obsidian folder), and then had Obsidian open the vault in that location from my primary computer. My secondary folder has a similar shared folder, and once the vault folder populated there, I had obsidian open the vault in that folder.
I may try uninstalling obsidian from the secondary computer and trying again, maybe it got confused since I may have had the vault open before the .obsidian folder got copied over. Other than that I’m not sure how to proceed.