Ok, so I have a so-so fix which isn't ideal but I will step through the process of my .htaccess file as best as I can for anyone else who might be facing the same problem:
# 404 ERROR
ErrorDocument 404 http://domain.com/404.html
Options +FollowSymLinks
RewriteEngine On
# REMOVES "www."
RewriteCond %{HTTP_HOST} ^www\.(.+)$ [NC]
RewriteRule ^(.*)$ http://%1%{REQUEST_URI} [R=301,L]
# REDIRECTS domain.html TO domain/ ~ REMOVED SO CMS CAN FIND ORIGINAL FILE
# RewriteCond %{THE_REQUEST} ^[A-Z]{3,9}\ /index\.html\ HTTP/
# RewriteRule ^index\.html$ http://domain.com/ [R=301,L]
# ADDS TRAILING SLASH "/" to URL
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_URI} !(.*)/$
RewriteRule ^(.+)$ /$1/ [L,R=301]
# REWRITE something.html TO SHOW AS something/ CMS CAN FIND ORIGINAL FILE
RewriteCond %{DOCUMENT_ROOT}/$1.html -f
RewriteRule ^(.+)/$ /$1.html [QSA,L]
# REWRITE something.php TO SHOW AS something/ CMS CAN FIND ORIGINAL FILE
RewriteCond %{DOCUMENT_ROOT}/$1.php -f
RewriteRule ^(.+)/$ /$1.php [QSA,L]
# REDIRECTS something.html TO something/ ~ REMOVED SO CMS CAN FIND ORIGINAL FILE
# RewriteCond %{ENV:REDIRECT_STATUS} ^$
# RewriteRule ^(.+)\.html$ /$1 [R=301,L]
# RewriteCond %{ENV:REDIRECT_STATUS} ^$
# RewriteRule ^(.+)\.php$ /$1 [R=301,L]
So, in short to allow Pagelime access to original files but still use pretty URLs your .htaccess file would look something like this:
# Redirect 404 Error
ErrorDocument 404 http://domain.com/404.html
Options +FollowSymLinks
RewriteEngine On
# Remove www
RewriteCond %{HTTP_HOST} ^www\.(.+)$ [NC]
RewriteRule ^(.*)$ http://%1%{REQUEST_URI} [R=301,L]
# Add trailing slash
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_URI} !(.*)/$
RewriteRule ^(.+)$ /$1/ [L,R=301]
# View .html and .php files without extension
RewriteCond %{DOCUMENT_ROOT}/$1.html -f
RewriteRule ^(.+)/$ /$1.html [QSA,L]
RewriteCond %{DOCUMENT_ROOT}/$1.php -f
RewriteRule ^(.+)/$ /$1.php [QSA,L]
You must include a <base href="http://domain.com/" /> below your <title></title> tags in the head to make the CSS work for pretty URLs, don't ask me why!
This isn't an ideal situation as it leads to duplicate content, being accessed from something/ and something.html which could harm SEO ranking ... however it's a quick fix until I can figure out how to exlude an IP from a given mod_rewrite statement.
Hope this makes sense, pass on to anyone who needs it!
Rob :)