Hi Ryan,
Could you please check that you have set in your order statuses not to send emails?
These are located in '
CMS Desk -> Tools ->
E-commerce >-Configuration -> Order status'.
If you have set to send email in this statuses, emails will be set even if you uncheck mentioned checkboxes.
So if your desired final step will be
completed, you can set to send emails only for this status.
Best Regards,
Zbysek Nemec.