Problems while migrating drupal website from localhost to server
To avoid requiring ?q=user or ?q=some/page/path you should assure ModRewrite is enabled on your Apache webserver. If you're on shared hosting you made need to ask your host provider to enable this module of Apache.
Moving a Drupal site is essentially moving all the PHP + MySQL data from 1 computer to another. Pick you're tools: mysqldump + zip, rsync, scp, ftp ... Drush whatever ... but the procedure is essentially the same -- move everything in it's entirety.


Why you have 2 less tables between your Drupal installs is unfortunately simply bad project management on your behalf -- good luck tracking down the differences.

Comparing drush pm-list between the 2 Drupal installs should help to find any modules on 1 system and not on the other. I like using drush archive-dump and drush archive-restore to move Drupal sites around -- but under your time constraint I recommend using SQL migration tools and code migration tools your comfortable and most familiar with.