Domain name in url multiple times - joomla

Question

Domain names show up thrice after malware removal. I disable SEF in the configuration.php and this reduced the domain name to twice in URL. But the URLs are messed up. But links are still showing twice and menu items are showing thrice.
eg example.com/example.com/example.com/index.php/about-us
Of course, this stops images from showing up and somehow links (even though wrong) are still loading the text content from the supposed pages, without images of course - this is only with SEF disabled.
The site uses Joomla how should I go about fixing this? Also, I cannot access the administrator area I am guessing because of the same issue so I am working with the file manager.
This is my htaccess
##
# #package Joomla
# #copyright Copyright (C) 2005 - 2015 Open Source Matters. All rights reserved.
# #license GNU General Public License version 2 or later; see LICENSE.txt
##
##
# READ THIS COMPLETELY IF YOU CHOOSE TO USE THIS FILE!
#
# The line just below this section: 'Options +FollowSymLinks' may cause problems
# with some server configurations. It is required for use of mod_rewrite, but may already
# be set by your server administrator in a way that disallows changing it in
# your .htaccess file. If using it causes your server to error out, comment it out (add # to
# beginning of line), reload your site in your browser and test your sef url's. If they work,
# it has been set by your server administrator and you do not need it set here.
##
## No directory listings
IndexIgnore *
## Can be commented out if causes errors, see notes above.
# For security reasons, Option followsymlinks cannot be overridden.
#Options +FollowSymlinks
Options +SymLinksIfOwnerMatch
Options -Indexes
## Mod_rewrite in use.
RewriteEngine Off
## Begin - Rewrite rules to block out some common exploits.
# If you experience problems on your site block out the operations listed below
# This attempts to block the most common type of exploit `attempts` to Joomla!
#
# Block out any script trying to base64_encode data within the URL.
RewriteCond %{QUERY_STRING} base64_encode[^(]*\([^)]*\) [OR]
# Block out any script that includes a <script> tag in URL.
RewriteCond %{QUERY_STRING} (<|%3C)([^s]*s)+cript.*(>|%3E) [NC,OR]
# Block out any script trying to set a PHP GLOBALS variable via URL.
RewriteCond %{QUERY_STRING} GLOBALS(=|\[|\%[0-9A-Z]{0,2}) [OR]
# Block out any script trying to modify a _REQUEST variable via URL.
RewriteCond %{QUERY_STRING} _REQUEST(=|\[|\%[0-9A-Z]{0,2})
# Return 403 Forbidden header and show the content of the root homepage
RewriteRule .* index.php [F]
#
## End - Rewrite rules to block out some common exploits.
## Begin - Custom redirects
#
# If you need to redirect some pages, or set a canonical non-www to
# www redirect (or vice versa), place that code here. Ensure those
# redirects use the correct RewriteRule syntax and the [R=301,L] flags.
#
## End - Custom redirects
##
# Uncomment following line if your webserver's URL
# is not directly related to physical file paths.
# Update Your Joomla! Directory (just / for root).
##
RewriteBase /
## Begin - Joomla! core SEF Section.
#
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
#
# If the requested path and file is not /index.php and the request
# has not already been internally rewritten to the index.php script
RewriteCond %{REQUEST_URI} !^/index\.php
# and the requested path and file doesn't directly match a physical file
RewriteCond %{REQUEST_FILENAME} !-f
# and the requested path and file doesn't directly match a physical folder
RewriteCond %{REQUEST_FILENAME} !-d
# internally rewrite the request to the index.php script
RewriteRule .* index.php [L]
#
## End - Joomla! core SEF Section.

Answer 1

I fixed the issue by changing the live site URL in the configuration.php from example.com to http://example.com. I was able to reenable SEF after that and everything works.
I realized when looking at the source code that the URLs were correct but where they lead to was incorrect. Which then lead me to recheck the config file for the millionth time and I just tried the change above and it worked!