Windchill licenses installation

Are you using the wcadmin or your Windchill administrator account? And it cannot see the license UI on the Site page? Screen shots please of what you see. This account should have been part of the license exclusion group.

Can you clarify which menu is missing?

Most likely someone applied licensing to default Site Administrator account identified by the property...

xconfmanager -d wt.admin.defaultAdministratorName

If so, you have to remove that licensing at the database level before you can get the UI back.

User to group relationship mapping...

For SQL Server it looks like this...  Update the bold red text accordingly.

declare @wcuser NVARCHAR(60)
set @wcuser='mjones'
select wtu.name as 'user', wtg.name as 'group', ml.idA2A2 from WTUser wtu, WTGroup wtg, MembershipLink ml where wtu.idA2A2=ml.idA3B5 and wtg.idA2A2=ml.idA3A5 and wtu.name=@wcuser
union all
select wtu.name as 'user', lp.name as 'group', ml.idA2A2 from WTUser wtu, LicenseProfile lp, MembershipLink ml where wtu.idA2A2=ml.idA3B5 and lp.idA2A2=ml.idA3A5 and wtu.name=@wcuser
union all
select wtu.name as 'user', sp.name as 'group', ml.idA2A2 from WTUser wtu, StandardProfile sp, MembershipLink ml where wtu.idA2A2=ml.idA3B5 and sp.idA2A2=ml.idA3A5 and wtu.name=@wcuser

Returns

user      group                           idA2A2

Remove your site administrator account from any "PTC *" license group and the "License Exclusion" group.

-- Delete relationship between user and group/profile
delete from MembershipLink where idA2A2='1103501';

Restart Windchill and try again.