Let it run. I saw the exact same thing -- eventually Aperture finished. As long as iStat reports 100% of one core, just let it run. If you bring up the OS X Force Quit window, I think you'll see that Aperture is NOT marked "not responding".
I had to move a Library from a USB 3 drive to FW800, and it runs _much_ slower. Once you have your Library working, I recommend moving it to USB 3 (if you can). This seems to be a recent change: with 3.3, USB 3 was not significantly faster than FW800.