bmossavari & GauGau:
Okay thanks. Yes I have the knowledge and experience to do it correctly from a shell. Which is even more exasperating since the cPanel doesn't give me the control I need. I did originally try FTP-ing, but didn't want to overlay the original directory (it is all backed up now), but it kept failing and terminating and I never knew for sure if all of the files got there.
But the main question I needed answered is "upgrade" only, so now I just have to find a technical way around getting all of the files up there in the correct format and location.
BTW, I am new to this whole mysite.com building and administering (came from a client-server unix world). Can you please clarify "anycontent.php" files? Do you mean these would be files that I created? Where might they be located? I don't have any "find" ability so...
While I'm at it, can I ask why 777? I got hit with a worm and I tell you I don't like 777? 775 is bad enough. :-)