How do I accurately position a video made from an image sequence ?

Hi,
I have made a video from sequence of images taken at The Macula's "Luminous Flux" show.
These images ( over 100 of them ) are the same view at different stages of the show, I know I should have shot this as video in the first place.

I cannot get the video to align perfectly in the panorama, it should do as I can use any one of them in the pano creation.
Any help on setting parameters to make it fit would be appreciated.

Pano can be viewed here http://www.jeffstarley.com/luminous_flux/ where you can see the (slight but annoying) mis-alignment,
as well as the other problems, which I can fix.

Thanks for your time.
Jeff