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Move upload() and uploadChunk() into the Helper with the following signature:

upload: function(component, helper file, fileContents) {...},

uploadChunk : function(component, helper, file, fileContents, fromPos, toPos, attachId) {... }

(notice we added the 'helper' arg)

In save() call upload() like this:

helper.upload(component, helper, file1, fileContents);

In upload(), call uploadChunk() like this:

helper.uploadChunk(component, helper, file, fileContents, fromPos, toPos, '');

In uploadChunk(), call uploadChunk() like this:

helper.uploadChunk(component, helper, file, fileContents, fromPos, toPos, attachId);

You may also want to take a look at this blog post to see how you can encapsulate the file upload logic in a reusable JS file: https://developer.salesforce.com/blogs/developer-relations/2016/12/lightning-components-code-sharing.html