To filter the activation email message, you can use the "wpmu_signup_user_notification_email" filter. You can find more information on this hook here: http://xref.wordpress.org/trunk/WordPress/Multisite/_wp-includes---ms-functions.php.html#functionwpmu_signup_user_notification (it's a WordPress hook).
You'll note the hooks for "wpmu_signup_user_notification_subject" in the same function which can be used for updating the "subject" of the email. It does not appear to be currently possible to modify the email.
1 - When Gravity Forms 1.7 is released, it will be providing a new way to create and manage form notifications. We have plans to update how the User Registration activation email is sent to integrate with this system and it will be completely customizable.
In the meantime, I've added a task in our PMS to look into a method for providing the activation link as a merge tag as a stop gap solution until then. No ETA, but I've included this thread in the task details so it will be updated when this is completed.
2 - I tested on a regular WP install and a multi-site install. I received the follow up login email in both cases. Are you running a plugin or applying any filters that cancel the default login notification sent to users after signup by WordPress? This is all hooked into default WP functionality.
3 - We wanted to keep this as integrated as possible with WP default functionality. Being unable to alter the from email address and from name on the notification apparently is a WP limitation. You're right though. Once we look into provide the activation link as a merge tag, this won't be an issue.
Bear in mind, due to the order of events... it *may* not be possible to create an activation link merge tag. I'll keep you posted.
Posted 7 years ago on Friday September 28, 2012 | Permalink