I've been testing ClouSE and I really like it. I started with the AMI with Linux, MySQL and ClouSE (not yappix), added nginx, WordPress , WP2Cloud etc etc.
Importing my site using WordPress Tools->Import also works fine, images are moved to S3, the only problem is that the image urls in posts and pages aren't updated (they still point to wp-content/uploads..)
So ... my suggestion is, and I believe this is the quickest fix ref your "migration tool", that you create your ClouSE Import plugin, accessible from Tools->Import :)
PerS - http://soderlind.no/