if I add field at the end of users table for keeping separate auto_increment,
will it interfere in anyway with your code?
Just set up $dbUserShema's indexes of setup_options.php properly - miniBB should work fine with any fields order and positions.
Admin has its own separate folder with copy of the forum.
This is kind of weird thing you definitely did wrong. Now what? For upgrading the forum, you need to upgrade 2 copies. Basically, I don't even understand why you need the second copy just for the admin.
It just seems you are doing a lot of noise on your own instead of buying 3 hours of our work and avoid any problems in the future :-) Anyway... it's your business.
Hey man you got any sort of script for adding moderators instead of going to the script and edditing it?
We don't have any tool for that so far.