That is indeed one of the use cases that I had in mind for Poio API. You might also be able to do this with XML transformations, but in Poio API it's just a matter of creating edges between nodes on the parent tier and the child tier. It is still not very convenient, but I wrote a short script that points you in the direction:
https://gist.github.com/pbouda/6220175You might still want to remove the regions from the nodes (as they are not time-aligned in your new.eaf, as far as I see) and then change the linguistic types of the tiers. Let me know if I can help with anything, from here on.
Best,
Peter