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I'm not sure of the sequence of your experience reported here.
Was your site already installed on the internet/intranet and you edited the files when you upgraded? Or did you edit the files before you installed? I presume you already had a working site? And if it was working, were you trying to upgrade when it quite working?
For myself, I guess that I would try to upload all the core files to your site first, make sure the site is set up and working right before editing the layout/theme/templates/etc. After it's working right and you've backed it up, then begin editing the files. Make sure you get it working as it is intended before making changes. As you track the changes and amke them samll and one-by-one, you'll know where it went wrong and be able to back up. Also, make a MySQL and data backup before making the changes, too. For the moment, though, just getting the core (except mainfile.php) up to your site, loaded and working should get the admin up and running.
It's possible (probable???) I've misunderstood entirely what you're saying/asking.
Wishing you luck.
MMM...It tastes like chicken! ...