Perseverance! :) For any that may have had the same issue as me (missing templates or improper linking)... be sure that you check the following!

My issue was in configuration!
@balihr has a great post on how to set up your cpanel for subdomains (http://www.zen-cart.com/showthread.p...630#post822630)

Next have a look at your configure file.. make sure you don't have the subdirectory entered in the catalog definition. It should've pointed to just '/' in my case because I am already pointing to the shop directory in the cpanel redirect. You may have to check your own set up, but when I put in shop after using the cpanel to redirect to shop, it wasn't right. :)

If you copy the following, be sure to delete the ">>>>>>>>>>>>>>>>>>>> " I am only using it to show you what to look at.
$template_dir = "site2";
define('SITE_NAME','site2');
define('HTTP_SERVER', 'http://shop2.mysite.com');
>>>>>>>>>>>>>>>>>>>>>>>define('DIR_WS_CATALOG', '/');
>>>>>>>>>>>>>>>>>>>>>>>define('DIR_WS_HTTPS_CATALOG', '/');
define('STORE_NAME','storename'); //Store Name

define('CATEGORIES_ROOT','7'); //root categories is 1 for this site