I'm afraid I don't know what an .htaccess file is (even after a bit of reading!) I know that the set up (in terms of the file structure) is exactly as it was before the upgrade, because I just copied the root Jay-moss.com folder, deleted it and then re-uploaded it.
the full error message i'm getting is this:
"The requested URL /archives/category/commercial was not found on this server.
Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request."
And it appears for every path other than jay-moss.com, i've tried restoring the MySQL database from different days in the same database but nothing seems to change?
Also: I if I create a new post category in WP dashboard, it will show up in the category list on the front page, but then also give the above error when you try and click through (i'd figured that at least newly created pages would work but it seems not)?