Do you have that djConfig variable in your 'index-release-version.html'? It looks like Dojo is trying to find init.js at ../Integralist/Init.js, but you somehow need to tell it to look in ../Classes/Init.js
This is what your modulePaths : {'Integralist' : '../Classes'} was doing in your Index.html....
I'd suggest working from the repo I linked to from my blog post (http://github.com/rmurphey/dojo-scaffold) -- I double-checked that it's definitely working :) -- and make changes to it until your changes break something, rather than trying to create your own structure right off the bat.
At a glance, I'm not 100% clear why you've got a Dojo.js file inside your directory structure, (is this the base Dojo lib or something else?), but the rest of Dojo is located elsewhere. If you use the structure I proposed, you can safely remove the djConfig declaration when using the built files, but as Dan mentioned, you may need to keep it if you're using a different configuration.