Build ember-cli app without Ember

I have a web page that has multiple ember apps on it. I'm using Ember-cli for all of them. Each is attached to a different rootElement. To cut down on the load size, I'd like to build the apps and exclude Ember.js from the final result. Then I can include (atleast, I think I can) include it separately instead of loading it three times.

In ember-app.js, I've commented out:

'ember.js': {
    development: defaultDevelopmentEmber,
    production:  this.bowerDirectory + '/ember/ember.prod.js'
    },

which has given some of the desired result. Ember.js is no longer in vendor.js, but when I do that, I get the following errors:

Error: Could not find module jquery
TypeError: Ember.Application is undefined 
TypeError: Ember.DefaultResolver is undefined

I'm going to assume that's because the modules aren't being loaded properly through the compiler, but I'm not certain how to fix it. Is this possible or is there a better alternative? Thanks