Thanks for the extra information!
After reviewing that, it seems to me that the source of the problem may be some difference between using a full domain instead of a subdomain as indicated in the wiki article (though I don't really think it should make a difference, that is one thing that differs between your method and that described in the wiki).
Also, since a permissions problem was indicated, I'm wondering if your two domains are "owned" by two different *nix users? That may also be part of the problem.
Finally, I believe that wiki article was written some time ago, and DH new "extra user security" setting may have something to do with your problem. Check the users' setup in the control panel and see if either of the users (if there are more than one) have this option enabled,; that might have something to do with all this.
Frankly I'm not at all sure how, or if, PHP-CGI is impacted by symlinks, or whether or not that could have anything to do with your problem (I'm only mentioning it as a point for research if you still can't get it to work).
At some point, you might consider that you can always repeat the "custom install process" on the second domain as a "workaround" until you can get it all sorted - with your DH quotas, there's no significant "hit" for duplicating the PHP installation.
I'm sorry I don't have a "OH! That's the problem; here is what you need to do" kind of answer for you. While I have used custom PHP installs before, I usually have my domains set up to run as different users, and I have never attempted to have them "share" a PHP installation - if I need a custom install, I just install one for each domain (often they need different settings anyway!).