Sierra: swap control & command key?

Thanks for using Apple Support Communities, PeterWeter!
Congratulations on your new iMac! I see that your iMac on macOS Sierra isn't allowing you to change your key options. Since I've been typing most of my adult life, not being able to use any key the way I'd like would slow me down. I'll be glad to help.
Try safe mode if your Mac doesn‘t finish starting up -- Starting in safe mode is a great way to make sure everything's starting up correctly.

What is safe mode?

Safe mode (sometimes called safe boot) is a way to start up your Mac so that it performs certain checks, and prevents some software from automatically loading or opening. Starting your Mac in safe mode does the following:

• Verifies your startup disk, and attempts to repair directory issues if needed
• Loads only required kernel extensions
• Prevents Startup Items and Login Items from opening automatically
• Disables user-installed fonts
• Deletes font caches, Kernel cache and other system cache files

Once your iMac starts in safe mode, you should be able to set your keyboard keys the way you'd like.

Cheers!

Good morning, PeterWeter. Thanks for that information. ​Since it's working in single-user mode, you'll want to check the login items you have set. macOS Sierra: If you think you have incompatible login items -- This article will help you isolate the culprit.

Have a great day!

In case you haven't found a working answer yet, Karabiner-Elements deos the job impeccably.

https://github.com/tekezo/Karabiner-Elements

You can swap the ctrl and command keys like so:

https://www.dropbox.com/s/fk0qjkdnrmf280e/Screenshot%202016-10-16%2015.02.46.png ?dl=0