I think you are overthinking things here
If you move your database and directory and rerun the install script and use the proper information for your new site on the install every last thing will be reinstalled correctly on the new server integrated with the live site. Remember your installing essentially on a new server and this is how you set everything through the script.
Only way your going to have issues is if you run the install script and do not put in the proper information. We ask for cookie prefix, forum url table prefix etc all on the install. I recommend following the instructions I posted from the beginning to the letter.
Obviously you are not updating everything in a manual capacity which is why I never recommended you do that.