Change JIRA to AD integration and expiring non-directory users

We have a long standing JIRA (6.1) installation with about 1000 users that has grown over time. As an AD environment, I'd like to integrate JIRA with AD with the end result being that only users in the AD environment remain active users.

I've added Active Directory as a second user directory and synchronized successfully but have not promoted it to the #1 directory spot yet.

What are the steps needed to :

1. Start using the AD direcotry without breaking user history, assigned tickets, filters, etc. etc.
2. Expire accounts in the internal directory and not in AD

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