Could you let us know what method you used to complete the installation on EasyApache 3? Note that you may want to consider purchasing CloudLinux, as it offers Mod Passenger support for EA4:
alt-mod-passenger for EasyApache 4 updated
I ended up just doing it the normal way, i.e.
Everything worked OK and migrating did not mess up anything with Phusion Passenger or Ruby. I might add that I use RVM (Ruby Version Manager) to install and update Ruby. Not sure if that matters or not.
I did have some custom user Apache includes that needed to be manually moved to new location. The migration does not do this automatically. I knew this before migration but what I did not know is where to put them after migration. I could not find anything in the docs that said where the new location should be. I might be somewhere and I just missed it. Anyway, i finally figured it out and user account includes should go in:
/etc/apache2/conf.d/userdata/std/2_4/<user account>/user conf.conf
/etc/apache2/conf.d/userdata/ssl/2_4/<user account>/user conf.conf
The migration will also not move over any Apache includes (Pre main, Pre virtualhost, and Post virtualhost). These need to be set again after migration.