Buuuump!

I've started dabbling with this project again, and have hit a snag: I'm trying to conform the geometry of the blu-ray scan with that of the scan used for the HDTV broadcast. Timing wise clips match up perfectly, however the geometry of the frame is somewhat different due to the different scans.

Does anyone have some advise on how I would be able to align the two video clips successfully using After Effects? This is important as a lot of the blu-ray footage is missing highlight and shadow information due to it being clipped out by the colorist.