I think the quickest way to get to the bottom of the permission denied 404 errors is if you can open a trouble ticket with ftp information as well as admin access to the site (preferably yours since you are getting the error when trying to update your signature). With that I should be able to do a bit of debugging to see exactly what's going on.
As for the zip file. Basically, the importer zip for classic had 2 files, ultimatebb.php and ultimatebb.cgi. If you open those up they are pretty heavily commented on what you need to change. THe ultimatebb.php script will go into the original ubb directory, and the ultimatebb.cgi script will go into your cgi directory that held the original classic scripts.
Once those are in place the search engines should redirect from the old links to the new ones as well.
