I've had to rebuild my sites recently due to a hit on the Drupalgeddon bug I thought I closed. I've been trying to migrate everything in easily but it doesn't seem to want to for whatever reason.
I realize this is almost a year after your original post and you most likely have resolved the issue already but in case you are still having issues with Drupageddon fallout, try this bash shell script which can help you recover your site. See https://github.com/uberhacker/drupalgetem. Let me know if this helps or if you are still having trouble migrating your site.