Hi Pete,
Nice work, getting to the bottom of this 
.
Are there any changes you would recommend us making to the install guide to avoid this next time.
The changes you mentioned to apache2.conf in your link look identical to the changes mentioned in the install guide:
Emoncms uses a front controller to route requests, modrewrite needs to be configured:
sudo a2enmod rewrite
For `<Directory />` and `<Directory /var/www/>` change `AllowOverride None` to `AllowOverride All`. This may be on lines 7 and 11 of `/etc/apache2/sites-available/default`. Modern versions of Ubuntu store these in the main config file: `/etc/apache2/apache2.conf`.
sudo nano /etc/apache2/sites-available/default
or
sudo nano /etc/apache2/apache2.conf
[Ctrl + X ] then [Y] then [Enter] to Save and exit.
Restart the lamp server:
sudo service apache2 restart
Did you follow these steps?
Why are the changes you made to htaccess required? Following symlinks should not be needed. Unless you symlinked the files into your web directory. Would you recommend these changes be made default?