Migrate from Ember Start Kit (not appkit) to Ember.cli

I have a node.js backend server and an ember front-end project which is together:

public\js -> contains all the ember app stuff
app\ -> contains the node.js files
server.js -> main express server code

I would like to migrate to use ember-cli. I've tried the migrator and running ember init but both do not really work and give me errors. Most the documentation talks about migrating from EmberAppKit which I didn't use, but use my own grunt script to complie the templates and uglify and minify the css and js files.

How should I go about migrating such a project to Ember-cli? I'm very confused..please help.

Thanks!