Ok, no answers here. I'll answer it myself... I just emailed Gunnar Thalin (author of DeShaker). He said that he doesn't think that DeShaker could be used for this, as it can't directly detect the movement of black borders. Detecting the movement of sprocket holes would only be possible if they were very well defined -- the ones from my SW film are typically rather faint and thus appear to flicker when moving from frame to frame. DeShaker is designed to aggregate the movement of a larger mass of RGB content.
He was kind enough to look at a small section of the test grab I did last night, and on that formed the above conclusion.