Thanks for the compliments on the avatar. I've always been fond of this one.
You could try the following for the sites:
#newsite <nbr>
#name "name"
#end
#selectsite <nbr>
#homecom <monster number>
#homecom <monster number>
#homemon <monster number>
#end
That will give you monsters that are only recruitable by the original owner (your new nation). #homecom allows recruitment of commanders, #homemon allows recruitment of line units. Check the commands from the mod manual (since my memory could be playing tricks on me). I know they work, because I've used them extensively when testing units for the DB.
Remember, you can assign a maximum of 5 properties per site (e.g. 2 types of gems + 1 unit + 2 commanders or any other combination).
The reason I suggested the seemingly convoluted approach above is that the first mod commands actually create the site, the second set then modifies its properties and the second set is the one that is known to work for certain.
See if that will clear up the rest of your problems.