Why aren't my internal links working - apache

Question

Basically, without this code in my .htaccess file, none of my internal links on my site work.
But with it in my .htaccess file, I am recieving a ton of HTTP/1.1 500 errors and a few 302 errors.
This is the code:
RewriteCond %{REQUEST_URI} !^/index\.php
RewriteRule .* index.php [L]
I tried changing %{REQUEST_URI} to %{HTTP_HOST}. That fixed the internal link problem, but the errors are still there.
How would I modify this to remove all the errors I am receiving, and so that my internal links work?
PS. My site in built in Joomla.
If needed, this is my full .htaccess file":
Options +FollowSymLinks
<FilesMatch "\.(ico|jpg|jpeg|png|gif|js|css|swf)$">
<IfModule mod_expires.c>
ExpiresActive on
ExpiresDefault "access plus 30 days"
</IfModule>
Header unset ETag
FileETag None
</FilesMatch>
RewriteEngine On
RewriteCond %{QUERY_STRING} base64_encode[^(]*\([^)]*\) [OR]
RewriteCond %{QUERY_STRING} (<|%3C)([^s]*s)+cript.*(>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} GLOBALS(=|\[|\%[0-9A-Z]{0,2}) [OR]
RewriteCond %{QUERY_STRING} _REQUEST(=|\[|\%[0-9A-Z]{0,2})
RewriteRule .* index.php [F]
RewriteCond %{HTTP_HOST} !^(m)\.candoboatloans\.com\.au
RewriteCond %{HTTP_HOST} !^www\.candoboatloans\.com\.au
RewriteRule (.*) http://www.candoboatloans.com.au/$1 [R=301,L]
Options +FollowSymLinks
RewriteCond %{THE_REQUEST} ^.*/index\.php
RewriteCond %{HTTP_HOST} !^(m)\.candoboatloans\.com\.au/index.php
RewriteRule ^(.*)index.php$ http://www.candoboatloans.com.au/$1 [R=301,L]
RewriteRule ^(.*)\.htm$ $1.html [L]
#RewriteBase /
RewriteCond %{HTTP_HOST} !^/index\.php
RewriteRule .* index.php [L]
# Check if mobile=1 is set and set cookie 'mobile' equal to 1
RewriteCond %{QUERY_STRING} (^|&)mobile=1(&|$)
RewriteRule ^ - [CO=mobile:1:%{HTTP_HOST}]
# Check if mobile=0 is set and set cookie 'mobile' equal to 0
RewriteCond %{QUERY_STRING} (^|&)mobile=0(&|$)
RewriteRule ^ - [CO=mobile:0:%{HTTP_HOST}]
# cookie can't be set and read in the same request so check
RewriteCond %{QUERY_STRING} (^|&)mobile=0(&|$)
RewriteRule ^ - [S=1]
# Check if this looks like a mobile device
RewriteCond %{HTTP:x-wap-profile} !^$ [OR]
RewriteCond %{HTTP_USER_AGENT} "android|blackberry|iphone|ipod|iemobile|opera mobile|palmos|webos|googlebot-mobile" [NC,OR]
RewriteCond %{HTTP:Profile} !^$
# Check if we're not already on the mobile site
RewriteCond %{HTTP_HOST} !^m\.
# Check to make sure we haven't set the cookie before
RewriteCond %{HTTP:Cookie} !\mobile=0(;|$)
# Now redirect to the mobile site
RewriteRule ^ http://m.candoboatloans.com.au%{REQUEST_URI} [R,L]

Answer 1

Give this a try, its based of joomla's default .htaccess with the needed parts from your .htaccess:
<FilesMatch "\.(ico|jpg|jpeg|png|gif|js|css|swf)$">
<IfModule mod_expires.c>
ExpiresActive on
ExpiresDefault "access plus 30 days"
</IfModule>
Header unset ETag
FileETag None
</FilesMatch>
#####################################################
# READ THIS COMPLETELY IF YOU CHOOSE TO USE THIS FILE
#
# The line just below this section: 'Options +FollowSymLinks' may cause problems
# with some server configurations. It is required for use of mod_rewrite, but may already
# be set by your server administrator in a way that disallows changing it in
# your .htaccess file. If using it causes your server to error out, comment it out (add # to
# beginning of line), reload your site in your browser and test your sef url's. If they work,
# it has been set by your server administrator and you do not need it set here.
#
#####################################################
## Can be commented out if causes errors, see notes above.
Options +FollowSymLinks
#
# mod_rewrite in use
RewriteEngine On
# Uncomment following line if your webserver's URL
# is not directly related to physical file paths.
# Update Your Joomla! Directory (just / for root)
RewriteBase /
# Check if mobile=1 is set and set cookie 'mobile' equal to 1
RewriteCond %{QUERY_STRING} (^|&)mobile=1(&|$)
RewriteRule ^ - [CO=mobile:1:%{HTTP_HOST}]
# Check if mobile=0 is set and set cookie 'mobile' equal to 0
RewriteCond %{QUERY_STRING} (^|&)mobile=0(&|$)
RewriteRule ^ - [CO=mobile:0:%{HTTP_HOST}]
# cookie can't be set and read in the same request so check
RewriteCond %{QUERY_STRING} (^|&)mobile=0(&|$)
RewriteRule ^ - [S=1]
# Check if this looks like a mobile device
RewriteCond %{HTTP:x-wap-profile} !^$ [OR]
RewriteCond %{HTTP_USER_AGENT} "android|blackberry|iphone|ipod|iemobile|opera mobile|palmos|webos|googlebot-mobile" [NC,OR]
RewriteCond %{HTTP:Profile} !^$
# Check if we're not already on the mobile site
RewriteCond %{HTTP_HOST} !^m\.
# Check to make sure we haven't set the cookie before
RewriteCond %{HTTP:Cookie} !\mobile=0(;|$)
# Now redirect to the mobile site
RewriteRule ^ http://m.candoboatloans.com.au%{REQUEST_URI} [R,L]
# Redirect to www if not www.domain or m.domain
RewriteCond %{HTTP_HOST} !^(m)\.candoboatloans\.com\.au
RewriteCond %{HTTP_HOST} !^www\.candoboatloans\.com\.au
RewriteRule (.*) http://www.candoboatloans.com.au/$1 [R=301,L]
# If it ends with index.php and is not m.domain redirect to www.domain.com/content
RewriteCond %{THE_REQUEST} ^.*/index\.php
RewriteCond %{HTTP_HOST} !^(m)\.candoboatloans\.com\.au$
RewriteRule ^(.*)index.php$ http://www.candoboatloans.com.au/$1 [R=301,L]
# Redirect all variations of index and default to www.domain.com/
# exception of index.php which should not be redirect
RewriteCond %{THE_REQUEST} ^[A-Z]{3,}\s/+(default|index)\.(s?html?|pl|aspx?|cfm)[\s]+ [NC]
RewriteRule ^ /? [R=301,L]
########## 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 set a mosConfig value through the URL
RewriteCond %{QUERY_STRING} mosConfig_[a-zA-Z_]{1,21}(=|\%3D) [OR]
# Block out any script trying to base64_encode crap to send via URL
RewriteCond %{QUERY_STRING} base64_encode.*\(.*\) [OR]
# Block out any script that includes a <script> tag in URL
RewriteCond %{QUERY_STRING} (\<|%3C).*script.*(\>|%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})
# Send all blocked request to homepage with 403 Forbidden error!
RewriteRule ^(.*)$ index.php [F,L]
#
########## End - Rewrite rules to block out some common exploits
########## Begin - Joomla! core SEF Section
#
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !^/index.php
RewriteCond %{REQUEST_URI} (/|\.php|\.html|\.htm|\.feed|\.pdf|\.raw|/[^.]*)$ [NC]
RewriteRule (.*) index.php
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization},L]
#
########## End - Joomla! core SEF Section