That's sad, but you have much more work than I expected. You have a Standalone CA which isn't suited for large environments, automation and so on. It is really impractical to use this type of CA in AD environment. Standalone CAs are used as offline Root/Policy CAs that issue certificates only to other CAs.
This means that you will have to reinstall CA from scratch. First of all, you will need to remove CA role from server and perform AD cleanup from CA objects as per this article: https://social.technet.microsoft.com/wiki/contents/articles/3527.how-to-decommission-a-windows-enterprise-certification-authority-and-how-to-remove-all-related-objects.aspx
Then you will have to install new CA and choose "Enterprise CA" CA type in wizard.
And the last note: never install CA on domain controllers. Because you will be stuck with this DC. You cannot move/replace your DC if CA is installed there.