Apache RewriteRule Regex issue - rewriting url to point to external site - wordpress

Question

I have posted a similar question earlier that got answered and I believed it to solve this issue, but sadly it didn't.
I own two websites, where I am using one as a multisite WordPress site and the other as a site to redirect traffic from.
Updated .htaccess for secondary site:
RewriteEngine On
RewriteCond %{HTTP_HOST} ^(www\.)?secondary.com$ [NC]
RewriteRule ^(.*)$ http://primary.com/secondary/$1 [P]
And this .htaccess on my primary site:
# BEGIN WordPress
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]
RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) $2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.(php|js|css|woff|ttf|svg))$ $2 [L]
RewriteRule . index.php [L]
# END WordPress
AddType x-httpd-php54 .php
At first glance, it seems to be working fine, but there are two main issues:
All links on the site seem to be pointing towards http://secondary.com/secondary/article-title instead of http://secondary.com/article-title and when I click on one of them I get redirected to http://primary.com/secondary/article-title. I think there's something wrong with my RewriteRules, but I am uncertain of where - anyone have a clue?
The rewrite doesn't seem to work in IE11 on Windows 8 or Chrome on a mobile device - it redirects instead. How could this be? And how can I fix it?
I'm fairly sure this has an easy solution to someone who knows what he/she is doing, but personally I am rather clueless when it comes to Apache, so any help with it would be greatly appreciated.