HDR Panorama Stitching (Photo Merge)

Hi,
Over the last few years I have generated a series of images to be converted in to a HDR Panorama.
i.e. Tripod mounted camera, take 3 exposure levels, rotate camera, repeat until scene is complete.
The problem I've found is that you can stitch, or you can HDR, but doing both tends to lead to problems. (normally alignment)
The solution occurred to me earlier, stitch the 0 exposure using PS Photomerge, then using the same masks, replace the images with the +/- exposures and I'll be able to generate 3 perfectly aligned stitched images, that can then be HDR'd.
The problem comes that PS rotates the images during alignment.
Is there anyway to duplicate the rotation on to a different series of images for the above purpose?
Either that, or can anyone suggest an alternative for my intended purpose?

I can't say as I have ever had a problem, but I would have used Photomatix for the HDR sets, and then merged the saved TIFFs in Photoshop.  What is your current workflow?

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