WordPress Nav Menu Items Broken on localhost - wordpress

I'm having major issues with my local development version of a client's site.
I've been working on their blog section and began getting 404 errors when using the pagination links for categories, or posts by author.
After doing some research the most common solution seemed to be to go to WP Admin Area and reset the permalink settings. So I did that, and that is where the fun really began.
Now, none of the nav menu items work at all. If I click any of them I get a 404 error - although they don't render the 404.php file, just a generic page with "NOT FOUND The requested URL /Clients/blah-blah-blah/index.php was not found on this server."
Looking further into it the most recommended course of action is to amend the .htaccess file, which I have, but to no avail.
At present, the .htacess file has:
**ErrorDocument 404 /404.php
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /Clients/Bubs%20World%20Dev/
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /Clients/Bubs%20World%20Dev/index.php [L]
</IfModule>
# END WordPress**
I've tried other solutions along the same lines but they don't seem to work.
If anyone has any ideas on this it would be greatly appreciated.
Thanks in advance,
Don

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I am trying to redesign a website from a friend and it's chaotic as hell. Now I am stuck a bit.
The old domain it something like http://www.website.com/folder/
I am trying the get rid out of the "folder", so I changed the setting in the wordpress setting and the root in the web-provider. The whole website is working fine, also the Wordpress admin area. But if I'm trying to get into the "home" page, it won't load - or it is loading endlessly.
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A piece often forgotten is the .htaccess file (found in the root of your WP install); I especially suspect it because you're going from a subfolder to no subfolder.
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# BEGIN WordPress
<IfModule mod_rewrite.c>
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I am working on the site: http://cancerhope.com/
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<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress
Nothing seems to work.
Strange thing is that the blog page works:
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The actual article that we have there works to:
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######BEGIN SwiftSecurity######
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# END WordPress
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I think this might be more of a webhosting problem. Probably your hoster automatically redirects subdomain.domain.tld to domain.tld/subdomain if the subdomain is not found.
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http://wordpress.org/support/topic/404-pages-not-working-1
http://wordpress.org/support/topic/404-pages-not-working
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