Cannot get certificate 404 error [Solved]

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Juergen,
I am switching from a ClearOS server to my new Ubuntu server, so the other certificate is from the old one.
I am configuring the Ubuntu one to be pretty much the same.
What I am getting slightly confused with is how the config file and the physical web root interact. The procedure I am following to set up email assumes you are hosting on an ISP provided server and that your domain is a virtual one. My DNS records point the remote.gscomputing.co.uk domain to the root website which is on /var/www/html which seems to be different to older Ubuntu servers was just /var/www I think.
I created the folder /var/www/remote.gscomputing.co.uk and then when I created the site it added public_html and entered the usual default index.html page.

It seems to be working because if you browse to http://remote.gscomputing.co.uk you do see the default Apache page.

I then added /.well-known/acme-challenge/
Because it wasn’t working I tried changing the /etc/apache2/sites-available/remote.gscomputing.co.uk.conf file to this:

<VirtualHost *:80>
	ServerName remote.gscomputing.co.uk
	DocumentRoot /var/www/html/
</VirtualHost>

Origonally it was:

<VirtualHost *:80>
	ServerName remote.gscomputing.co.uk
	DocumentRoot /var/www/remote.gscomputing.co.uk
</VirtualHost>

So I am confused as to what is going on?

Following some of the other support messages on here I tested being able to access a file in /.well-known/acme-challenge/ so I created a 1234 file in there and if you browse to:

http://remote.gscomputing.co.uk/.well-known/acme-challenge/1234 it will display a blank page so I know you can see that? So I am baffled as to why Lets Encrypt is getting a 404 error?

Is it some sort of permissions issues. I have set the ownership of the whole tree as follows:
sudo chown www-data:www-data /var/www/remote.gscomputing.co.uk -R

In the procedure I am following I am told that the www-data user is the Apache user hence why it needs permissions.

Thanks for your help.