Finally figured this one out with a two part answer. Putting this here to help future troubleshooters:
To get rid of the old disabled users that were showing up I just needed to refine the LDAP Search Directory Root to point to our current users OU instead of the one above it that included all of our inactive users as well.
To get the machine to show the newer addresses that were missing, I noticed in the User Mappings options the Email Address field was not properly mapped to the users' email address and instead was coming up null. Pointing that field to UserPrincipalName brought in email addresses and voila! Search on the machine is now working.