Thanks for the suggestion Kevin but unfortunately the Anti-flicker Filter is having no effect on this problem at all.
Any other suggestions would be greatly appreciated...
I've heard good things about Tinderbox FurnaceCore Deflicker.
Otherwise, it will take so much time to composite that you're better off reshooting.
Sorry, but this is one of the nastiest things to just "fix it in post."
If you can't reshoot... track & replace 'em in Ae with the 3d camera tracker.