I haven’t necessarily resolved the iframe issue, but I did get it to work another way. I’m using sequenceserver via passenger and then loading it via ajax into drupal as recommended here http://stackoverflow.com/questions/4366103/how-to-use-an-iframe-into-drupal
I think this setup would still have problems if the document.domain were different, but luckily using passenger lets it load on the same server.
-Colin