For anyone who comes across this in the future, here are the steps to get the game from C2 -> Windows 8 (steps 3 & 4 might not be necessary for you):
1) Export to Windows 8
2) Open the sln file in VS 2012
3) Add the Windows Library for Javascript 1.0 reference (C2 was trying to use it RC version for me)
3a) Remove the .RC from the WinJS references in index.html
4) Add windows app store publisher name to the <identity> tag in package.appxmanifest (should be something like CN=YourName)
5) Download clay.io/api/api.js, clay.io/api/api.css, clay.io/socket.io.js
6) Shift + Alt + A to add existing scripts, select the 3 you just downloaded
7) Include in index.html the following (inside <head></head> works, just needs to be before c2runtime.js):
<link rel='stylesheet' href='api.css' />
<script src='socket.io.js'></script>
<script src='api.js'></script>