[eluser]bramb79[/eluser]
If you are already stuck with the directories, copying the index.php is probably your best bet.
As for the problems:
You can make your code conditional (by detecting the domain url) and load either specific config files (you can add your own config files and overwrite certain config variables) or stick with the standard config files (and just make certain variables conditional (like your base_url).
Redirecting to the right controller can best be done in the routing file (see clooner's post).
