Hi,
If I understand well, you modified your login chain to add AD and remove NTLM.
So that gives you 2 options:
1- add the NTLM in your login chain
Both AD and NTLM can coexist. Having both would enable you to invite external users for example and would reenable the admin account.
2- Add you new admin as a site manager.
To do so, browse to the admin panel > groups
Then search for the group: "<name of your site> (site_<name of your site>)"
Inside it you should have the 4 groups for the 4 permissions. Find the site_<name of your site>_manager and add your new admin there.
This will make your new admin user be automatically a manager of the site of your choice