One of the challenges I faced is that I could not find where to override Drupal 6 Installation theme, which is "minelli" and "garland".

Well, over here:

• /includes/theme.maintenance.inc, all occurrences of themes/garland and minnelli are to be overwritten!
• /modules/system/system.install, lines 372 -376
• /modules/update/update.module, all occurrences of themes/garland