Create and pre-populate a mutiple value field in field collection on new node with ajax call
Ok so I didn't manage to solve this directly, but I did accomplish my intent behind this quesion.

The intent behind this was to pre-populate a field collection from another node on a node create form with an ajax call.

I'm still not sure how you alter the fields in a field collection on a form and I'll leave this question open in case anyone knows, however if you're looking to pre-populate field collections onto a node, then this blog post has an answer:

http://drupal.cocomore.com/blog/field-collections-exposed

And I posted an example using ajax to do this in an answer to this question (where I think it's more relevant): How to create (&amp; pre-populate) multiple “field collection” fields on an ajax call