How can I replace the Joomla! Registration link?

The standard Joomla! Registration link goes to the Joomla! Registration form (or possibly to a custom form in your template).To make the link go to a ChronoForm the best solution is to use a 'template override'.This is a Joomla! feature that lets you over-ride many of the standard features without changing the core code.
 
You create a template override by adding a file in the templates/your_template/html/ folder. The standard Registration form is in the file components/com_users/views/registration/tmpl/default.php The equivalent override file will be templates/your_template/html/com_users/registration/default.php
 
If there is already a file with this name then rename it to default.old.php. Create a new empty default.php and add this code in CFv4:
<?php
$mainframe =& JFactory::getApplication();
$mainframe->redirect('index.php?option=com_chronoforms&chronoform=my_form_name');
?>
Or this code in CFv5:
<?php
$app = JFactory::getApplication();
$app->redirect('index.php?option=com_chronoforms5&chronoform=my_form_name');
?>
Save the file and test to make sure that the redirection takes place correctly.

See a Joomla! help document on template over-rides here.

To edit a file you can either use a local text editor and upload the new file or a Joomla! extension like exTplorer that will allow you to edit files from the Site Admin.