Unless you uploaded everything in binary instead of using ascii for text based files then that shouldn't be a problem..
What are you using to edit the drupal files? If its notepad,wordpad, or something similar I would suggest trying Chrimson Editor, it supports saving unix style files. http://www.crimsoneditor.com/
It is probably from dos style line endings causing problems, just resave any files you edited previously as unix style files and upload them again.
Yes, settings.php has taken the place of conf.php
Hope that helps