First of all, I would like to point out that Thunder can create an Empty Custom Module inside its own assembly, which contains the self-installing code as described in the blog post. You do not need to do it manually.
Now, about your question. Have you tried using Sitefinity Thunder's new Code Deploy functionality? You can use it to register them manually for you, or you can use it just to copy your assemblies over and let them register their own modules, which is the better option in my opinion. You can use the module's Install/Upgrade/Initialize methods to install or register everything which your custom module requires. Please note that Code Deploy requires you to have a Site Sync license.
If you do not have a Site Sync license, you will need to copy the assemblies manually.