I don?t know if this is a help for you, but I left the admin-folders in each of the catalog folders, adjusting the respective configure and database_table files, so that I finally have 3 (in your case) admin-sections. So I can assign a specific shop_ID to every store.
By the way, I just realize that you have THREE stores, not 2. Your ..._store1 is already store 2.
Also, in every catalog- and the catalog/admin-folder you need to readjust 2 more files, that are:
database_table.php
define('TABLE_CONFIGURATION', 'configuration');
to
define('TABLE_CONFIGURATION', 'configuration_store1');
AND
configure
replace all occurencies of 'catalog' with 'catalog_store2' or whatever you called the folder where you put your second store into.
Hope this helps.