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Yup, xoops_version.php is very important to go through, but don't go in the trap of thinking that just because you have changed things there, then everything is alright.
One other thing: When you change the template names, you will also need to change the code in the php files, setting the template to use. It is done with this line:
$xoopsOption['template_main'] = "template_name";
where you of course will need to change it to the new name.
If, on the other hand, you don't intend to have different templates in the modules, you can also completely remove the templates directory and the lines regarding templates from xoops_version.php, then the templates used will be the ones form the original module (also meaning, that if you change the template in one clone, you will also change it in other clones)
