Most of this is way above my pay grade so I won't be offended if someone steps in and says I'm going down a completely wrong path.
My first question is whether anything is working? Are you trying to get a previously working (primary) domain up after making the changes to accommodate multisites or is the problem with the subsite? Or are you working from a fresh install?
At first glance it seems to me that manifestbuilder.php is the file that brings in all the other pieces of SS, and if it is kicking back on cms then it's telling you that it can't load it. I would look at that folder, if you're working from a fresh install, it's possible that the permissions were changed or the file itself was somehow corrupted during the upload or unpacking process. It should only take a minute to reload it and try again.
Since you say that you haven't had any problem installing SS before, my second step would be to re-check what you did to go from a working version to watching scandir across your screen. Banal's instructions were fabulous and invaluable, but when I was researching a solution for my problem I found that everybody seemed to have to do things slightly differently to get things to work. Some people had to change permissions, alter the htaccess or add a cache folder, others didn't. I can't imagine how anything in the instructions would leave you unable to load, but who knows.
Sorry I can't be more helpful, but my errors were related to permissions, file location and a misinterpretation of the code for the symlink. All things that are relatively easy to trace and well within my scope...