I do HDR panoramas, too; but my workflow is completely different:
At the field, I always use a tripod, so the different exposures from each camera position all match perfectly. Later when dealing with the files, I create one panorama for each exposure, and then merge them into a HDR; these are the steps I follow:
First, I copy all the files from the first exposure to file1, file2, file3... . Then I create a LDR panorama with Hugin, and call it pano1. Without closing Hugin, I copy all the files from the second exposure over file1, file2, file3..., execute the same panorama and save it as pano2.
With this technique, I obtain a stack of panoramas pano1, pano2, pano3, ... perfectly aligned, that I can handle with enfuse / pfstools normaly. There is a longer description here:
http://edu-perez.blogspot.com/2008/12/panoramica-nocturna-de-barcelona-en-hdr.html, but I am afraid it is written in Spanish.
Hope this helps,
Edu.