Save auto-align parameters for batch processing?

I plan to shoot timelapse with two supposedly identical camera setups and stack images from the two cameras. Unfortunately the two lenses turn out not to be quite identical, so I need to correct/map images from one camera to match the field of view of the other. A test showed that Photoshop's auto-align procedure can do the mapping sufficiently accurate. So now what I want to do is to have Photoshop calculate the mapping parameters once, then apply that projection identically to a batch of images. What I really hope to avoid is for Photoshop to recalculate the mapping separately for every single frame, both because it is a huge waste of time but also because the exact same mapping really should be applied to all images. Is there a way to do this, CS6?
Thank you,
Poul

Thank you Noel. At least that means I can focus my effort elsewhere. If I have to do the transforms manually I will do it in After Effects. I think that will be somewhat easier (applies to whole sequence at once), especially since I will be editing/grading the timelapse sequences in there later anyway. The Photoshop auto-align did a better job than my manual attempt in After Effects though. The two lenses are circular fisheyes so heavy distortion makes it difficult. Another possible option is PanoTools - if I can get that figured out... Thanks again for your input!
-Poul

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